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At least 1,369 records · Page 76

Structures of Cryptococcus neoformans Protein Farnesyltransferase Reveal Strategies for Developing Inhibitors That Target Fungal Pathogens

Cryptococcus neoformans is a fungal pathogen that causes life-threatening infections in immunocompromised individuals, including AIDS patients and transplant recipients. Few antifungals can treat C. neoformans infections, and drug resistance is increasing. Protein farnesyltransferase (FTase) catalyzes post-translational lipidation of key signal transduction proteins and is essential in C. neoformans. We present a multidisciplinary study validating C. neoformans FTase (CnFTase) as a drug target, showing that several anticancer FTase inhibitors with disparate scaffolds can inhibit C. neoformans and suggesting structure-based strategies for further optimization of these leads. Structural studies are an essential element for species-specific inhibitor development strategies by revealing similarities and differences between pathogen and host orthologs that can be exploited. We, therefore, present eight crystal structures of CnFTase that define the enzymatic reaction cycle, basis of ligand selection, and structurally divergent regions of the active site. Crystal structures of clinically important anticancer FTase inhibitors in complex with CnFTase reveal opportunities for optimization of selectivity for the fungal enzyme by modifying functional groups that interact with structurally diverse regions. A substrate-induced conformational change in CnFTase is observed as part of the reaction cycle, a feature that is mechanistically distinct from human FTase. Our combined structural and functional studies provide a framework for developing FTase inhibitors to treat invasive fungal infections.

59 BASIC BIOLOGICAL SCIENCES↗

Flow and heat transfer measurements along a cooled supersonic diffuser

An experimental investigtion was conducted to ascertain the mean flowfield, including shock wave structure, separated flow regions, turbulent boundary-layer growth, static pressure variations, wall heat transfer, and shear stresses in a second-throat, axisymmetric, supersonic diffuser with wall cooling. The diffuser inlet Mach number of the heated air flow was 3.76, the stagnation pressure was 6.8 atm, the ratio of wall to total gas temperature was 0.44, and the diffuser discharged to the atmosphere. The complex flowfield involved deceleration and acceleration regions, supersonic and embedded subsonic regions, and strong viscous regions with relatively large radial and axial variations. The heat transfer and wall static pressure distributions were remarkably similar, and heat transfer rates were high locally at oblique shock/turbulent boundary-layer interactions, in the pseudoshock region, and in the separation region in the diffuser outlet section.

Back, L. H.↗

A viscous-inviscid interaction algorithm for three-dimensional turbulent subsonic aerodynamic juncture region flow

An order-of magnitude analysis of the subsonic, three-dimensional, steady time-averaged Navier-Stokes equations for semibounded aerodynamic juncture geometries yields the parabolic Navier-Stokes simplification. The numerical solution of the resultant pressure Poisson equation is cast into complementary and particular parts, yielding an iterative interaction algorithm with an exterior three-dimensional potential flow solution. A parabolic transverse momentum equation set is constructed, wherein robust enforcement first-order continuity effects is accomplished using a penalty differential constraint concept within a finite element solution algorithm. A Reynolds stress constitutive equation, with low turbulence Reynolds number wall functions, is employed for closure, using parabolic forms of the two-equation turbulent kinetic energy-dissipation equation system. The algorithm is employed to predict the three-dimensional turbulent flowfield in the juncture region formed by two intersecting parabolic arcs at a free-stream Mach-number of 0.08, and Re/C = 600,000/m.

Baker, A. J.↗

Langmuir probe theory and the problem of anisotropic collection

A more general understanding of Langmuir probe theory by going beyond particular coordinate systems as far as possible was studied. To delineate the role of initial velocities in the problem and to characterize the interaction between the velocity flow field and the electrostatic potential field both of which enter into the determination of particle trajectories are desired. The probe is supposed to be negatively charged throughout and the ensuing region of positive space charge about it differs fundamentally from the plasma region beyond in the sense that the former represents a region in which deterministic trajectories dominate while the lattice is a region dominated by statistical interactions largely controlled by the collisionless stationary Boltzmann equation. A general solution of this Boltzmann equation is given and its relationship to the problem of saturation current density in 3D is elucidated.

Kyrala, A.↗

Thermal transpiration: A molecular dynamics study

Thermal transpiration is a phenomenon where fluid molecules move from the cold end towards the hot end of a channel under the influence of longitudinal temperature gradient alone. Although the phenomenon of thermal transpiration is observed at rarefied gas conditions in macro systems, the phenomenon can occur at atmospheric pressure if the characteristic dimensions of the channel is less than 100 nm. The flow through these nanosized channels is characterized by the free molecular flow regimes and continuum theory is inadequate to describe the flow. Thus a non-continuum method like molecular dynamics (MD) is necessary to study such phenomenon. In the present work, MD simulations were carried out to investigate the occurance of thermal transpiration in copper and platinum nanochannels at atmospheric pressure conditions. The mean pressure of argon gas confined inside the nano channels was maintained around 1 bar. The channel height is maintained at 2nm. The argon atoms interact with each other and with the wall atoms through the Lennard-Jones potential. The wall atoms are modelled using an EAM potential. Further, separate simulations were carried out where a Harmonic potential is used for the atom-atom interaction in the platinum channel. A thermally insulating wall was introduced between the low and high temperature regions and those wall atoms interact with fluid atoms through a repulsive potential. A reduced cut off radius were used to achieve this. Thermal creep is induced by applying a temperature gradient along the channel wall. It was found that flow developed in the direction of the increasing temperature gradient of the wall. An increase in the volumetric flux was observed as the length of the cold and the hot regions of the wall were increased. The effect of temperature gradient and the wall-fluid interaction strength on the flow parameters have been studied to understand the phenomenon better.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Study of the material of the ATLAS inner detector for Run 2 of the LHC

The ATLAS inner detector comprises three different sub-detectors: the pixel detector, the silicon strip tracker, and the transition-radiation drift-tube tracker. The Insertable B-Layer, a new innermost pixel layer, was installed during the shutdown period in 2014, together with modifications to the layout of the cables and support structures of the existing pixel detector. The material in the inner detector is studied with several methods, using a low-luminosity √s=13 TeV pp collision sample corresponding to around 2.0 nb -1 collected in 2015 with the ATLAS experiment at the LHC. In this paper, the material within the innermost barrel region is studied using reconstructed hadronic interaction and photon conversion vertices. For the forward rapidity region, the material is probed by a measurement of the efficiency with which single tracks reconstructed from pixel detector hits alone can be extended with hits on the track in the strip layers. The results of these studies have been taken into account in an improved description of the material in the ATLAS inner detector simulation, resulting in a reduction in the uncertainties associated with the charged-particle reconstruction efficiency determined from simulation.

47 OTHER INSTRUMENTATION↗

Transition Heat Transfer Modeling Based on the Characteristics of Turbulent Spots

While turbulence models are being developed which show promise for simulating the transition region on a turbine blade or vane, it is believed that the best approach with the greatest potential for practical use is the use of models which incorporate the physics of turbulent spots present in the transition region. This type of modeling results in the prediction of transition region intermittency which when incorporated in turbulence models give a good to excellent prediction of the transition region heat transfer. Some models are presented which show how turbulent spot characteristics and behavior can be employed to predict the effect of pressure gradient and Mach number on the transition region. The models predict the spot formation rate which is needed, in addition to the transition onset location, in the Narasimha concentrated breakdown intermittency equation. A simplified approach is taken for modeling turbulent spot growth and interaction in the transition region which utilizes the turbulent spot variables governing transition length and spot generation rate. The models are expressed in terms of spot spreading angle, dimensionless spot velocity, dimensionless spot area, disturbance frequency and Mach number. The models are used in conjunction with a computer code to predict the effects of pressure gradient and Mach number on the transition region and compared with VKI experimental turbine data.

Simon, Fred↗

Wave and Particle Interactions in the High and Low-Altitude Auroral Region During Rising Solar Activity

The project has resulted in four separate investigations, which are each in various stages of publication in the refereed scientific journals. The first investigation was of the generation of electrostatic electron cyclotron waves observed by the Polar spacecraft throughout the auroral regions, dayside cusp, and polar magnetosphere. We have since discovered that these waves are also present within the magnetopause and magnetosheath, which is one of the topics of a second study, entitled: 'Polar observations of plasma waves in and near the dayside magnetopause/magnetosheath.' A third study of plasma waves focussed on kilometric continuum (KC) emission. This work is reported in a paper entitled 'Near-source and Remote Observations of Kilometric Continuum Radiation From Multi-spacecraft Observations'.The final investigation of this program concerns the possible transverse heating of auroral ions by impulsive wave structures. We summarize that substantial transverse ion heating has already occurred at lower altitudes. Abstracts of the above four studies are included in the Appendix to this final report.

Gurnett, Donald A.↗

Density Anomalies in the Mantle and the Gravitational Core-Mantle Interaction

Seismic studies suggest that the bulk of the mantle is heterogeneous, with density variations in depth as well as in horizontal directions (latitude and longitude). This density variation produces a three- dimensional gravity field throughout the Earth. On the other hand, the core density also varies in both time and space, due to convective core flow. Consequently, the fluid outer core and the solid mantle interact gravitationally due to the mass anomalies in both regions. This gravitational core-mantle interaction could play a significant role in exchange of angular momentum between the core and the mantle, and thus the change in Earth's rotation on time scales of decades and longer. Aiming at estimating the significance of the gravitational core-mantle interaction on Earth's rotation variation, we introduce in our MoSST core dynamics model a heterogeneous mantle, with a density distribution derived from seismic results. In this model, the core convection is driven by the buoyancy forces. And the density variation is determined dynamically with the convection. Numerical simulation is carried out with different parameter values, intending to extrapolate numerical results for geophysical implications.

Kuang, Weijia↗

Gravitational independence of single-breath washout tests in recumbent dogs

The effect of gravitational orientation in the mechanism of lung filling and emptying in dogs was examined by conducting simultaneously Ar-bolus and N2 single-breath washout tests (SBWTs) in 10 anesthetized dogs (prone and supine), with three of the dogs subjected to body rotation. Transpulmonary pressure was measured simultaneously, allowing identification of the lung volume above residual volume at which there was an inflection point in the pressure-volume curve. Combined resident gas and bolus SBWTs in recumbent dogs were found to be different from such tests in humans; in dogs, the regional distribution of ventilation was not primarily determined by gravity. The measurements did not make it possible to discern exact mechanisms of filling and emptying, but both processes appear to be related to lung, thorax, and mediastinum interactions and/or differences in regional mechanical properties of the lungs.

Tomioka, Shinichi↗

Interactions of amelogenin with phospholipids

Amelogenin protein has the potential to interact with other enamel matrix proteins, mineral, and cell surfaces. In this paper, we investigated the interactions of recombinant amelogenin rP172 with small unilamellar vesicles as model membranes, toward the goal of understanding the mechanisms of amelogenin–cell interactions during amelogenesis. Dynamic light scattering (DLS), fluorescence spectroscopy, circular dichroism (CD), and nuclear magnetic resonance (NMR) were used. In the presence of phospholipid vesicles, a blue shift in the Trp fluorescence emission maxima of rP172 was observed (~334 nm) and the Trp residues of rP172 were inaccessible to the aqueous quencher acrylamide. DLS studies indicated complexation of rP172 and phospholipids, although the possibility of fusion of phospholipids following amelogenin addition cannot be ruled out. NMR and CD studies revealed a disorder–order transition of rP172 in a model membrane environment. Strong fluorescence resonance energy transfer from Trp in rP172 to DNS-bound-phospholipid was observed, and fluorescence polarization studies indicated that rP172 interacted with the hydrophobic core region of model membranes. Finally, our data suggest that amelogenin has ability to interact with phospholipids and that such interactions may play key roles in enamel biomineralization as well as reported amelogenin signaling activities.

59 BASIC BIOLOGICAL SCIENCES↗

Geographic patterns of co-occurrence network topological features for soil microbiota at continental scale in eastern China

Soil microbiota play a critical role in soil biogeochemical processes and have a profound effect on soil functions. Recent studies have revealed microbial co-occurrence patterns in soil microbial communities, yet the geographic pattern of topological features in soil microbial co-occurrence networks at the continental scale are largely unknown. Here, we investigated the shifts of topological features in co-occurrence networks inferred from soil microbiota along a continental scale in eastern China. Integrating archaeal, bacterial and fungal community datasets, we inferred a meta-community co-occurrence network and analyzed node-level and network-level topological shifts associated with five climatic regions. Both node-level and network-level topological features revealed geographic patterns wherein microorganisms in the northern regions had closer relationships but had a lower interaction influence than those in the southern regions. We further identified topological differences associated with taxonomic groups and demonstrated that co-occurrence patterns were random for archaea and non-random for bacteria and fungi. Given that microbial interactions may contribute to soil functions more than species diversity, this geographic shift of topological features provides new insight into studying microbial biogeographic patterns, their organization and impacts on soil-associated function.

Environmental Sciences & Ecology↗

A knowledge brokerage approach for assessing the impacts of the setting up young farmers policy measure in Greece

This study explores Knowledge Brokerage (KB) aspects of an ex-post Impact Assessment (IA) for the Rural Development Programme (RDP) measure of setting up young farmers, under the Common Agricultural Policy (CAP), at the regional level in Northern Greece. The measure supports the entry of young farmers in agriculture by moving land from older to younger farmers. The aim of the study was to test a set of KB tools for improving the interaction between researchers and policy makers. Our analysis mainly focused on a suite of IA Support Modules to guide practitioners, and on a technical tool kit, a web-based contextualisation platform, to support the IA of the specific test case. Offering a structured approach towards IA, both the Support Modules and LIAISE-KIT allow framing the context, organisation, scheduling and method selection in the light of KB objectives. The evaluation of how IA Support Modules influence the Science Policy Interface (SPI), in the case of the ex-post assessment, demonstrated the high relevance of KB activities for facilitating the interaction between researchers and regional policy makers. The assessment bridges the gap between knowledge producers developing scientific output to be applied in a specific context, and knowledge users, who want clear messages regarding the policy challenges they face. Other conclusions include the need for specific guidelines and training for knowledge users, especially with regard to the use of tools. According to our findings, a consequent application of KB activities is a crucial pre-condition for successfully implementing IAs in future RDP measures.

54 ENVIRONMENTAL SCIENCES↗

Investigating the Causes and Impacts of Convective Aggregation in a High Resolution Atmospheric GCM

Abstract A ∼50 km resolution atmospheric general circulation model (GCM) is used to investigate the impact of radiative interactions on spatial organization of convection, the model's mean state, and extreme precipitation events in the presence of realistic boundary conditions. Mechanism‐denial experiments are performed in which synoptic‐scale feedbacks between radiation and dynamics are suppressed by overwriting the model‐generated atmospheric radiative cooling rates with its monthly varying climatological values. When synoptic‐scale radiative interactions are disabled, the annual mean circulation and precipitation remain almost unchanged, however tropical convection becomes less aggregated, with an increase in cloud fraction and relative humidity in the free troposphere but a decrease in both variables in the boundary layer. Changes in cloud fraction and relative humidity in the boundary layer exhibit more sensitivity to the presence of radiative interactions than variations in the degree of aggregation. The less aggregated state is associated with a decrease in the frequency of extreme precipitation events, coincident with a decrease in the dynamical contribution to the magnitude of extreme precipitation. At regional scales, the spatial contrast in radiative cooling between dry and moist regions diminishes when radiative interactions are suppressed, reducing the upgradient transport of energy, degree of aggregation, and frequency of extreme precipitation events. However, the mean width of the tropical rain belt remains almost unaffected when radiative interactions are disabled. These results offer insights into how radiation‐circulation coupling affects the spatial organization of convection, distributions of clouds and humidity, and weather extremes.

54 ENVIRONMENTAL SCIENCES↗

Prediction of nearfield jet entrainment by an interactive mixing/afterburning model

The development of a computational model (BOAT) for calculating nearfield jet entrainment, and its application to the prediction of nozzle boattail pressures, is discussed. BOAT accounts for the detailed turbulence and thermochemical processes occurring in the nearfield shear layers of jet engine (and rocket) exhaust plumes while interfacing with the inviscid exhaust and external flowfield regions in an overlaid, interactive manner. The ability of the model to analyze simple free shear flows is assessed by detailed comparisons with fundamental laboratory data. The overlaid methodology and the entrainment correction employed to yield the effective plume boundary conditions are assessed via application of BOAT in conjunction with the codes comprising the NASA/LRC patched viscous/inviscid model for determining nozzle boattail drag for subsonic/transonic external flows. Comparisons between the predictions and data on underexpanded laboratory cold air jets are presented.

Dash, S. M.↗

A Parametric Study of Jet Interactions with Rarefied Flow

Three-dimensional computational techniques, in particular the uncoupled CFD-DSMC of the present study, are available to be applied to problems such as jet interactions with variable density regions ranging from a continuum jet to a rarefied free stream. When the value of the jet to free stream momentum flux ratio approximately greater than 2000 for a sharp leading edge flat plate forward separation vortices induced by the jet interaction are present near the surface. Also as the free stream number density n (infinity) decreases, the extent and magnitude of normalized pressure increases and moves upstream of the nozzle exit. Thus for the flat plate model the effect of decreasing n (infinity) is to change the sign of the moment caused by the jet interaction on the flat plate surface.

Glass, C. E.↗

Aerosols, Chemistry, and Radiative Forcing: A 3-D Model Analysis of Satellite and ACE-Asia data (ACMAP)

We propose a research project to incorporate a global 3-D model and satellite data into the multi-national Aerosol Characterization Experiment-Asia (ACE-Asia) mission. Our objectives are (1) to understand the physical, chemical, and optical properties of aerosols and the processes that control those properties over the Asian-Pacific region, (2) to investigate the interaction between aerosols and tropospheric chemistry, and (3) to determine the aerosol radiative forcing over the Asia-Pacific region. We will use the Georgia TecWGoddard Global Ozone Chemistry Aerosol Radiation and Transport (GOCART) model to link satellite observations and the ACE-Asia measurements. First, we will use the GOCART model to simulate aerosols and related species, and evaluate the model with satellite and in-situ observations. Second, the model generated aerosol vertical profiles and compositions will be used to validate the satellite products; and the satellite data will be used for during- and post- mission analysis. Third, we will use the model to analyze and interpret both satellite and ACE- Asia field campaign data and investigate the aerosol-chemistry interactions. Finally, we will calculate aerosol radiative forcing over the Asian-Pacific region, and assess the influence of Asian pollution in the global atmosphere. We propose a research project to incorporate a global 3-D model and satellite data into

Chin, Mian↗