bluuebunny/crossref_metadata_2025 huggingface dataset:
Development of Efficient Small Scale Axial Turbine for Solar Driven Organic Rankine Cycle
Authors: Al Jubori Ayad , Al-Dadah Raya K. , Mahmoud Saad , Khalil Khalil M. , Bahr Ennil A. S.
Published: September 2016

Recently, the increase in fossil fuel consumption and associated adverse impact on the environment led to significant interest in renewable energy sources like solar. This paper presents a new methodology that integrates the ORC cycle analysis with modeling of an efficient small scale subsonic axial turbine at low temperature heat sources using wide range of organic working fluids like R123, R134a, R141b, R152a, R245fa, R290 and isobutene. The work involves detailed turbine analysis including 1D mean line approach, extensive 3D CFD simulations and ORC cycle analysis at inlet total pressure ranging from 2–5 bar corresponding to temperature range from 275K–365K to achieve the best turbine and cycle performance. This work provides a more reliable data base for small scale organic working fluids instead of using the map of large scale gas turbine.

The numerical simulation was performed using 3D RANS with SST turbulence model in ANSYS-CFX. Using iterative CFD simulations with various working fluids with subsonic inlet conditions, Mach number ranging from 0.6–0.65, results showed that using working fluid R123 for a turbine with mean diameter of 70mm, the maximum isentropic efficiency was 82% and power output 5.66 kW leading to cycle efficiency of 9.5%.
Defect Detection in an Annular Swirl-Burner-Array by Optical Measuring Exhaust Gases
Authors: von der Haar Henrik , Hartmann Ulrich , Hennecke Christoph , Dinkelacker Friedrich , Seume Joerg R.
Published: September 2016

Defects in combustion chambers of aircraft engines might have an impact on the reliability of the downstream turbine and the machine’s performance. Detecting failures in the combustion chamber of an aircraft engine during operation may improve the resource management and the availability of the system. Aim of the ongoing research project is to find an approach to evaluate the state of the jet engine by analyzing the temperature and emissions field in the exhaust jet.

This investigation is part of the collaborative research center SFB 871. The SFB 871 deals with the improvement of the regeneration process of complex capital goods such as aircraft engines. Maintenance, repair, and overhaul processes would be more efficient if the internal status of the engine would be known while still on the wing before it is disassembled.

The feasibility of this approach is investigated for a pilot scaled model combustor, which provides optical access and allows the selection of “defined errors” in the combustor. It consists of an atmospheric tubular combustor with an array of eight premixed swirl burners with a maximum output of 160 kW. The operating conditions of one of the eight burners concerning power and air-fuel ratio, can be controlled. A power distribution between the burners is typical fault in an aircraft combustor and will be investigated in this study. It is observed that it is possible to determine small deviations by measuring density profiles applying a tomographic background-oriented schlieren (BOS) technique behind the combustor. Additionally, particle image velocimetry is used to measure differences in the velocity field of the exhaust gases. This study shows that a minimum power deviation of one burner in an array of a total of eight burners is detectable in the exhaust plane with the above mentioned measurement techniques.
Experimental and Numerical Investigation of Direct and Indirect Combustion Noise Contributions in a Lean Premixed Laboratory Swirled Combustor
Authors: Kings Nancy , Tao Wenjie , Scouflaire Philippe , Richecoeur Franck , Ducruix Sébastien
Published: September 2016

Combustors are contributing to the core noise emission of aero-engines in terms of direct and indirect combustion noise. The first is caused by the unsteady heat release rate, the second by the acceleration of inflow inhomogeneities, such as entropy fluctuations, at the combustor outlet or in the turbine.

This work aims to investigate combustion noise generation mechanisms of a choked laboratory scale combustor by a combined experimental and numerical study. Therefore, the temperature fluctuations at the combustor outlet were determined experimentally as well as numerically and cross-checked together with pressure and OH* emission data in the frequency domain. A similar spectral content was found.

Furthermore, the acoustic and entropy fluctuations at the combustion chamber outlet were evaluated for different operation conditions to estimate the direct and indirect combustion noise contributions of a laboratory combustor.
Investigation of Bypass Transition in the Presence of a Separation Bubble With Tomographic PIV
Authors: Lyko Christoph , Michaelis Dirk , Peitsch Dieter , Dittmar Mirko
Published: September 2016

Low pressure turbines of small and medium sized engines may operate at very low Reynolds numbers. In consequence transition is delayed to an extend where laminar separation, detached transition and reattachment occur. The wakes from upstream blade rows lead to overall high turbulence levels which play a key role in the transition process. Freestream eddies buffeting the laminar boundary layer induce streamwise vortices known as Klebanoff Modes. To investigate this type of flow a flat plate was exposed to a pressure distribution. It is based on the PAK-B suction side and was created by a contoured wall facing the plate. The PAK-B is a Pratt & Whitney design and a Mach number scaled version of a highly aft loaded low pressure turbine airfoil. Due to the latter it suffers from a large separation bubble at low Reynolds numbers.

The flow has been intensively investigated by hot-wire anemometry with a very high spatial resolution. This allows obtaining very precise information about the location of characteristic flow areas; for instance the separation and reattachment positions. Based on this information, Tomographic PIV was employed to expose detailed features in specific areas of the flow field. This technique provides the velocity vector information inside a flow volume. It complements hot-wire results, which give a time resolved information but only planar velocity magnitudes. Combining these techniques and comparing their results is therefore an excellent way to raise the physical understanding of the flow behaviour. This has been done using velocity profiles, skin friction coefficients and integral boundary layer parameters. As the 3D-PIV information allows calculation of derived quantities, like the vector field rotation, a picture of the coherent structures can be drawn.
Low-Order Modeling of Nonlinear High-Frequency Transversal Thermoacoustic Oscillations in Gas Turbine Combustors
Authors: Hummel Tobias , Hammer Klaus , Romero Pedro , Schuermans Bruno , Sattelmayer Thomas
Published: September 2016

This paper analyzes transversal thermoacoustic oscillations in an experimental gas turbine combustor utilizing dynamical system theory. Limit cycle acoustic motions related to the first linearly unstable transversal mode of a given 3D combustor configuration are modeled, and reconstructed by means of a low order dynamical system simulation. The source of nonlinearity is solely allocated to flame dynamics, saturating the growth of acoustic amplitudes, while the oscillation amplitudes are assumed to always remain within the linearity limit. First, a Reduced Order Model (ROM), which reproduces the combustor’s modal distribution and damping of acoustic oscillations is derived. The ROM is a low-order state-space system, which results from a projection of the Linearized Euler Equations (LEE) into their truncated eigenspace. Second, flame dynamics are modeled as a function of acoustic perturbations by means of a nonlinear transfer function. This function has a linear and a nonlinear contribution. The linear part is modeled analytically from first principles, while the nonlinear part is mathematically cast into a cubic saturation functional form. Additionally, the impact of stochastic forcing due to broadband combustion noise is included by additive white noise sources. Then, the acoustic and the flame system is interconnected, where thermoacoustic non-compactness due to the transversal modes’ high frequency is accounted for by a distributed source term framework. The resulting nonlinear thermoacoustic system is solved in frequency and time domain. Linear growth rates predict linear stability, while envelope plots and probability density diagrams of the resulting pressure traces characterize the thermoacoustic performance of the combustor from a dynamical systems theory perspective. Comparisons against experimental data are conducted, which allow the rating of the flame modes in terms of their capability to reproduce the observed combustor dynamics. Ultimately, insight into the physics of high-frequency, transversal thermoacoustic systems is created.
Large Eddy Simulation of Soot Formation in a Model Gas Turbine Combustor
Authors: Koo Heeseok , Hassanaly Malik , Raman Venkat , Mueller Michael E. , Geigle Klaus Peter
Published: September 2016

The computational modeling of soot in aircraft engines is a formidable challenge, not only due to the multi-scale interactions with the turbulent combustion process but the equally complex physical and chemical processes that drive the conversion of gas-phase fuel molecules into solid-phase particles. In particular, soot formation is highly sensitive to the gas-phase composition and temporal fluctuations in a turbulent background flow. In this work, a large eddy simulation (LES) framework is used to study soot formation in a model aircraft combustor with swirl-based fuel and air injection. Two different configurations are simulated: one with and one without secondary oxidation jets. Specific attention is paid to the LES numerical implementation such that the discrete solver minimizes the dissipation of kinetic energy. Simulation of the model combustor shows that the LES approach captures the two recirculation zones necessary for flame stabilization very accurately. Further, the model reasonably predicts the temperature profiles inside the combustor. The model also captures variation in soot volume fraction with global equivalence ratio. The structure of the soot field suggests that when secondary oxidation jets are present, the inner recirculation region becomes fuel lean and soot generation is completely suppressed. Further, the soot field is highly intermittent suggesting that a very restrictive set of gas phase conditions promote soot generation.
Delayed Detached Eddy Simulation of Rotating Stall for a Full Annulus Transonic Axial Compressor Stage
Authors: Gan Jiaye , Im Hong-Sik , Zha Ge-Cheng
Published: September 2016

This paper solves the filtered Navier-Stokes equations to simulate stall inception of NASA compressor transonic Stage 35 with delayed detached eddy simulation (DDES). A low diffusion E-CUSP Riemann solver with a 3rd order MUSCL scheme for the inviscid fluxes and a 2nd order central differencing for the viscous terms are employed. A full annulus of the rotor-stator stage is simulated with an interpolation sliding boundary condition (BC) to resolve the rotor-stator interaction. The tip clearance is fully gridded to accurately resolve tip vortices and their effect on stall inception. The DDES results show that the stall inception of Stage 35 is initialized by a weak harmonic disturbance with the length scales of the full annulus and grows rapidly with two emerging spike like disturbance. The two spike disturbances propagate in counter rotational direction with about 42% of rotor speed. The spike stall cells cover about 6 blades. They lead to two stall cells grown circumferentially and inwardly.
Thermal Stability of Nickel-Base Alloys
Authors: Shifler D. A. , Sanchez L. , Kedir N. , Faucett D. , Mahapatra R. , Choi S. R.
Published: September 2016

The thermal stability of three Ni-base samples was assessed at 1850F (1010°C) and 2000F (1093°C) in ambient air as a function of exposure time ranging from 500 to 2000 hrs. Assessments of thermal stability of the samples were made using weight change, oxidation, microstructural evolution, and post-exposure mechanical properties such as Vickers microhardness and compressive yield stress. The three samples included bare Alloy “A” (9Cr-6Al-1.5Hf), Alloy “A” with an overlay coating, and bare Alloy “B” (12Cr-3Al), were not much different in compositions. At 1850F, oxidation as measured by weight change was insignificant up to 2000 h in all the three samples. At 2000F, however, noticeable weight change occurred, increasing linearly with time all in the three samples. The oxidation penetration from surface to matrix for these samples was more intense when exposed to above 1000 hours, forming various oxides, gamma-prime (γ′) depletion zones, and TCP phases. The size and area fraction of γ′ precipitates were determined as a function of temperature and exposure time. Post-exposure mechanical properties were also assessed through Vickers hardness and compressive yield stress. A maximum change in Vickers hardness was about 10% at both temperatures up to 2000 hrs. The change in compressive yield stress was more pronounced than the change in Vickers hardness as a function of thermal exposure and time.
Automated Thermal and Stress Preliminary Analyses Applied to a Turbine Rotor
Authors: Moret Maxime , Delecourt Alexandre , Moustapha Hany , Garnier Francois , Abenhaim Acher-Igal
Published: September 2016

The use of Multidisciplinary Design Optimization (MDO) techniques at the preliminary design phase (PMDO) of a gas turbine engine allows investing more effort at the pre-detailed phase in order to prevent the selection of an unsatisfactory concept early in the design process. Considering the impact of the turbine tip clearance on an engine’s efficiency, an accurate tool to predict the tip gap is a mandatory step towards the implementation of a full PMDO system for the turbine design. Tip clearance calculation is a good candidate for PMDO technique implementation considering that it implies various analyses conducted on both the rotor and stator. As a first step to the development of such tip clearance calculator satisfying PMDO principles, the present work explores the automation feasibility of the whole analysis phase of a turbine rotor preliminary design process and the potential increase in the accuracy of results and time gains. The proposed conceptual system integrates a thermal boundary conditions automated calculator and interacts with a simplified air system generator and with several conception tools based on parameterized CAD models. Great improvements were found when comparing this work’s analysis results with regular pre-detailed level tools, as they revealed to be close to the one generated by the detailed design tools used as target. Moreover, this design process revealed to be faster than a common preliminary design phase while leading to a reduction of time spent at the detailed design phase. By requiring fewer user inputs, this system decreases the risk of human errors while entirely leaving the important decisions to the designer.
Application of a Turbulent Jet Flame Flashback Propensity Model to a Commercial Gas Turbine Combustor
Authors: Kalantari Alireza , Sullivan-Lewis Elliot , McDonell Vincent
Published: September 2016

Because flashback is a key operability issue associated with low emission combustion of high hydrogen content fuels, design tools to predict flashback propensity are of interest. Such a design tool has been developed by the authors to predict boundary layer flashback using non-dimensional parameters. The tool accounts for the thermal coupling between the flame and burner rim and was derived using detailed studies carried out in a test rig at elevated temperature and pressure. The present work evaluates the applicability of the tool to a commercial 65 kW micro turbine generator (MTG). Two sets of data are evaluated. One set is obtained using the combustor, removed from the engine, which has been configured to operate like it does in the engine but at atmospheric pressure and various preheat temperatures. The second set of data is from a combustor operated as it normally would in the commercial engine. In both configurations, studies are carried out with various amounts of hydrogen added to either natural gas or carbon monoxide. The previously developed model is able to capture the measured flashback tendencies in both configurations. In addition, the model is used to interpret flashback phenomena at high pressures and temperatures in the context of the engine conditions. An increase in pressure for a given preheat temperature and velocity reduces the equivalence ratio at which flashback occurs and increases the tip temperature due to lower quenching distance. The dependency of the flashback propensity on the injector tip temperature is enhanced with an increase in pressure. The variation of critical velocity gradient with equivalence ratio for a constant preheat temperature is more pronounced at higher pressures. In summary, the model developed using the high pressure test rig is able to predict flashback tendencies for a commercial gas turbine engine and can thus serve as an effective design tool for identifying when flashback is likely to occur for a given geometry and condition.
Retracted: “Multi-Objective Aerodynamic Optimisation of a Real Gas Radial-Inflow Turbine” [ASME Turbo Expo 2016: Turbomachinery Technical Conference and Exposition, Volume 2C: Turbomachinery, Seoul, South Korea, June 13–17, 2016, Conference Sponsors: International Gas Turbine Institute, ISBN: 978-0-7918-4971-2, Copyright © 2016 by ASME. Paper No. GT2016-58132, pp. V02CT45A032; 9 pages; doi:10.1115/GT2016-58132]
Authors: ASME
Published: September 2016

The above referenced paper has been removed from publication. June 29, 2017.

Copyright © 2017 by ASME
Dynamical Properties of Combustion Instability in a Laboratory-Scale Gas-Turbine Model Combustor
Authors: Gotoda Hiroshi , Hayashi Kenta , Tsujimoto Ryosuke , Domen Shohei , Tachibana Shigeru
Published: September 2016

We present an experimental study on nonlinear dynamics of combustion instability in a lean premixed gas-turbine model combustor with a swirl-stabilized turbulent flame. Intermittent combustion oscillations switching irregularly back and forth between a burst and pseudo-periodic oscillations exhibit the deterministic nature of chaos. This is clearly demonstrated by considering two nonlinear forecasting methods: the extended version [1] of the Sugihara & May algorithm [2] as a local predictor, and the generalized radial basis function network as a global predictor [3], [4]. The former enables us to extract the short-term predictability and long-term unpredictability nature of chaos, while the latter can produce surrogate data to test for determinism as a free running approach. Permutation entropy is estimated by a symbolic sequence approach for the surrogate data to test for determinism and is also used as an online detector to prevent lean blowout.
LES Predictions of Jet Noise for a Pylon-Mounted Dual Stream Nozzle and Jet Surface Interactions
Authors: Vogel P. , Bin J. , Sinha N.
Published: September 2016

An end-to-end LES/FW-H noise prediction model has been demonstrated and validated with acoustic and flowfield data from a dual stream nozzle with pylon experiment conducted at NASA GRC using their Jet Engine Simulator (JES) geometry. Results show a large region of high turbulent kinetic energy (TKE) in the wake of the pylon. Acoustic Source Localization (ASL) studies using our numerical phased array methodology show this wake region to be the principle location of low frequency noise sources while higher frequency sources occur nearer to the nozzle lips. Numerical simulations have also been conducted on Jet-Surface Interaction (JSI) effects of a supersonic jet exhausting parallel to a finite surface. Time-averaged LES data and far-field noise predictions have been obtained for multiple surface locations as well as for an isolated jet nozzle. For upstream observers located below the surface, results show an increase in low-frequency noise over what was predicted for the isolated nozzle due to JSI effects and decrease in high-frequency noise due to shielding. This was significantly more pronounced for an over-expanded jet than for an under-expanded jet, an effect that was primarily attributed to the shorter core length of the over-expanded jet.
Technical Note: Multicenter study of TrueBeam FFF beams with a new stereotactic diode: Can a common small field signal ratio curve be defined?
Authors: Cagni Elisabetta , Russo Serenella , Reggiori Giacomo , Bresciani Sara , Fedele David , Iori Mauro , Marino Carmelo , Nardiello Barbara , Ruggieri Ruggero , Strigari Lidia , Mancosu Pietro
Published: September 2016

Purpose

Small radiation fields (<30 mm) are typically involved in stereotactic body radiation therapy procedures. Output factor measurements are subjected to large uncertainties. The signal ratio (SR) readings, defined as the ratio of central axis reading, respectively, in the actual field size and in the reference field size, were evaluated in several centers and a common mathematical description of the SR curve was investigated.

Methods

A couple of new unshielded stereotactic diodes (Razor, IBA) was tested under eight different TrueBeams using 10 MV flattering filter free beams with high dose rate (2400 MU/min). Small fields, ranging from 6 to 50 mm, were analyzed in terms of profiles and central axis point measurements. SRs were normalized to 30 mm field and were calculated as a function of nominal field size (NFS) and effective field size (EFS). From SRs acquired using Razor1 (four centers), a theoretical equation was extrapolated. Three centers with Razor2 were used to test the mathematical relationship. Finally, the two diodes were directly compared in the last center.

Results

The EFS was systematically smaller than NFS (p < 0.01) for all field size ranges, with mean difference of 0.9 ± 0.5 mm. The SR fits using the NFS and EFS had, respectively, R2 = 0.989 and R2 ≫ 0.999. The Razor2 centers’ mean deviation from the predicted SRs, using the NFS and EFS fits, was, respectively, 3.4% and 0.5%. The maximum deviations were 5.0% (6 mm field size) for NFS and 1.9% for EFS. Maximum deviation of 0.5% between the two Razors was observed.

Conclusions

EFS measurements were confirmed to be mandatory when comparing SRs over different centers. An equation establishing a functional relation between SRs and the EFS was obtained and tested for the new Razor diode.
Polyvinyl chloride as a multimodal tissue‐mimicking material with tuned mechanical and medical imaging properties
Authors: Li Weisi , Belmont Barry , Greve Joan M. , Manders Adam B. , Downey Brian C. , Zhang Xi , Xu Zhen , Guo Dongming , Shih Albert
Published: September 2016

Purpose

The mechanical and imaging properties of polyvinyl chloride (PVC) can be adjusted to meet the needs of researchers as a tissue‐mimicking material. For instance, the hardness can be adjusted by changing the ratio of softener to PVC polymer, mineral oil can be added for lubrication in needle insertion, and glass beads can be added to scatter acoustic energy similar to biological tissue. Through this research, the authors sought to develop a regression model to design formulations of PVC with targeted mechanical and multimodal medical imaging properties.

Methods

The design of experiment was conducted by varying three factors—(1) the ratio of softener to PVC polymer, (2) the mass fraction of mineral oil, and (3) the mass fraction of glass beads—and measuring the mechanical properties (elastic modulus, hardness, viscoelastic relaxation time constant, and needle insertion friction force) and the medical imaging properties [speed of sound, acoustic attenuation coefficient, magnetic resonance imaging time constants T1 and T2, and the transmittance of the visible light at wavelengths of 695 nm (Tλ695) and 532 nm (Tλ532)] on twelve soft PVC samples. A regression model was built to describe the relationship between the mechanical and medical imaging properties and the values of the three composition factors of PVC. The model was validated by testing the properties of a PVC sample with a formulation distinct from the twelve samples.

Results

The tested soft PVC had elastic moduli from 6 to 45 kPa, hardnesses from 5 to 50 Shore OOO‐S, viscoelastic stress relaxation time constants from 114.1 to 191.9 s, friction forces of 18 gauge needle insertion from 0.005 to 0.086 N/mm, speeds of sound from 1393 to 1407 m/s, acoustic attenuation coefficients from 0.38 to 0.61 (dB/cm)/MHz, T1 relaxation times from 426.3 to 450.2 ms, T2 relaxation times from 21.5 to 28.4 ms, Tλ695 from 46.8% to 92.6%, and Tλ532 from 41.1% to 86.3%. Statistically significant factors of each property were identified. The regression model relating the mechanical and medical imaging properties and their corresponding significant factors had a good fit. The validation tests showed a small discrepancy between the model predicted values and experimental data (all less than 5% except the needle insertion friction force).

Conclusions

The regression model developed in this paper can be used to design soft PVC with targeted mechanical and medical imaging properties.
Does orthographic training on a phonemic contrast absent in the listener's dialect influence word recognition?
Authors: Dufour Sophie , Nguyen Noël , Pattamadilok Chotiga , Frauenfelder Ulrich Hans
Published: September 2016

This study examined whether the ability of southern French speakers to discriminate between standard French word forms such as /pike/ and /pikε/ can be improved by a training procedure in which participants were exposed to the orthographic representations of words forming /e/-/ε/ minimal pairs. The results of the training procedure showed that southern French speakers were able to perceive the /e/-/ε/ contrast in word final position when they associated words containing these vowels with their correct spelled form. Further, participants in a priming experiment, which was run immediately after training, no longer showed the priming effect on the trained minimal pairs that they had shown in the pre-test. However, a priming effect on the untrained minimal pairs was still observed immediately after training, showing that this training failed to transfer to untrained items. Finally, the benefits of the training procedure were no longer observed the day after training, since southern French speakers once again showed a priming effect on the trained minimal pair of words in a one day post-test. Implications of these findings for the locus of the difficulties of the southern French speakers with the word-final /e/-/ε/ contrast are discussed.
Kirchhoff scattering from non-penetrable targets modeled as an assembly of triangular facets
Authors: Abawi Ahmad T.
Published: September 2016

Frequency and time domain solutions for the scattering of acoustic waves from an arbitrarily shaped target using the Kirchhoff approximation are developed. In this method, the scattering amplitude is analytically evaluated on a single triangle and scattering from a triangularly facetted target is computed by coherently summing the contributions from all the triangles that make up its surface. In the frequency domain, the solution is expressed in terms of regular (non-singular) functions, which only require the knowledge of the directions of the incident and scattered fields, the edge vectors for the triangles and position vectors to one of their vertices. To derive representations using regular functions in the time domain, the scattered signal is expressed by different expressions for various limiting cases. The frequency domain solution is validated by comparing its results to the solutions of problems for which the Kirchhoff approximation has analytic solutions. In order of increasing complexity, they include the square plate, the circular plate, the finite cylinder and the sphere. The time domain solution is validated by comparing it to the time domain solution of the Kirchhoff approximation for a rigid sphere.
From damage to discovery via virtual unwrapping: Reading the scroll from En-Gedi
Authors: Seales William Brent , Parker Clifford Seth , Segal Michael , Tov Emanuel , Shor Pnina , Porath Yosef
Published: September 2016

Computational virtual unwrapping of the En-Gedi scroll reveals it to be the earliest Pentateuchal book ever found in a Holy Ark.
Plant diversity patterns in neotropical dry forests and their conservation implications
Authors:   DRYFLOR, Banda-R Karina , Delgado-Salinas Alfonso , Dexter Kyle G. , Linares-Palomino Reynaldo , Oliveira-Filho Ary , Prado Darién , Pullan Martin , Quintana Catalina , Riina Ricarda , Rodríguez M. Gina M. , Weintritt Julia , Acevedo-Rodríguez Pedro , Adarve Juan , Álvarez Esteban , Aranguren B. Anairamiz , Arteaga Julián Camilo , Aymard Gerardo , Castaño Alejandro , Ceballos-Mago Natalia , Cogollo Álvaro , Cuadros Hermes , Delgado Freddy , Devia Wilson , Dueñas Hilda , Fajardo Laurie , Fernández Ángel , Fernández Miller Ángel , Franklin Janet , Freid Ethan H. , Galetti Luciano A. , Gonto Reina , González-M. Roy , Graveson Roger , Helmer Eileen H. , Idárraga Álvaro , López René , Marcano-Vega Humfredo , Martínez Olga G. , Maturo Hernán M. , McDonald Morag , McLaren Kurt , Melo Omar , Mijares Francisco , Mogni Virginia , Molina Diego , Moreno Natalia del Pilar , Nassar Jafet M. , Neves Danilo M. , Oakley Luis J. , Oatham Michael , Olvera-Luna Alma Rosa , Pezzini Flávia F. , Dominguez Orlando Joel Reyes , Ríos María Elvira , Rivera Orlando , Rodríguez Nelly , Rojas Alicia , Särkinen Tiina , Sánchez Roberto , Smith Melvin , Vargas Carlos , Villanueva Boris , Pennington R. Toby
Published: September 2016

Seasonally dry tropical forests are distributed across Latin America and the Caribbean and are highly threatened, with less than 10% of their original extent remaining in many countries. Using 835 inventories covering 4660 species of woody plants, we show marked floristic turnover among inventories and regions, which may be higher than in other neotropical biomes, such as savanna. Such high floristic turnover indicates that numerous conservation areas across many countries will be needed to protect the full diversity of tropical dry forests. Our results provide a scientific framework within which national decision-makers can contextualize the floristic significance of their dry forest at a regional and continental scale.
Convergent local adaptation to climate in distantly related conifers
Authors: Yeaman Sam , Hodgins Kathryn A. , Lotterhos Katie E. , Suren Haktan , Nadeau Simon , Degner Jon C. , Nurkowski Kristin A. , Smets Pia , Wang Tongli , Gray Laura K. , Liepe Katharina J. , Hamann Andreas , Holliday Jason A. , Whitlock Michael C. , Rieseberg Loren H. , Aitken Sally N.
Published: September 2016

When confronted with an adaptive challenge, such as extreme temperature, closely related species frequently evolve similar phenotypes using the same genes. Although such repeated evolution is thought to be less likely in highly polygenic traits and distantly related species, this has not been tested at the genome scale. We performed a population genomic study of convergent local adaptation among two distantly related species, lodgepole pine and interior spruce. We identified a suite of 47 genes, enriched for duplicated genes, with variants associated with spatial variation in temperature or cold hardiness in both species, providing evidence of convergent local adaptation despite 140 million years of separate evolution. These results show that adaptation to climate can be genetically constrained, with certain key genes playing nonredundant roles.
Gathering lots of data on a small budget
Authors: Greenville Aaron C. , Emery Nathan J.
Published: September 2016

Open-source hardware and software technology can redefine data collection
Balancing Trained Immunity with Persistent Immune Activation and the Risk of Simian Immunodeficiency Virus Infection in Infant Macaques Vaccinated with Attenuated Mycobacterium tuberculosis or Mycobacterium bovis BCG Vaccine
Authors: Jensen Kara , dela Pena-Ponce Myra Grace , Piatak Michael , Shoemaker Rebecca , Oswald Kelli , Jacobs William R. , Fennelly Glenn , Lucero Carissa , Mollan Katie R. , Hudgens Michael G. , Amedee Angela , Kozlowski Pamela A. , Estes Jacob D. , Lifson Jeffrey D. , Van Rompay Koen K. A. , Larsen Michelle , De Paris Kristina
Published: September 2016

Our goal is to develop a pediatric combination vaccine to protect the vulnerable infant population against human immunodeficiency virus type 1 (HIV-1) and tuberculosis (TB) infections. The vaccine consists of an auxotrophMycobacterium tuberculosisstrain that coexpresses HIV antigens. Utilizing an infant rhesus macaque model, we have previously shown that this attenuatedM. tuberculosis(AMtb)-simian immunodeficiency virus (SIV) vaccine is immunogenic, and although the vaccine did not prevent oral SIV infection, a subset of vaccinated animals was able to partially control virus replication. However, unexpectedly, vaccinated infants required fewer SIV exposures to become infected compared to naive controls. Considering that the current TB vaccine,Mycobacterium bovisbacillus Calmette-Guérin (BCG), can induce potent innate immune responses and confer pathogen-unspecific trained immunity, we hypothesized that an imbalance between enhanced myeloid cell function and immune activation might have influenced the outcome of oral SIV challenge in AMtb-SIV-vaccinated infants. To address this question, we used archived samples from unchallenged animals from our previous AMtb-SIV vaccine studies and vaccinated additional infant macaques with BCG or AMtbonly. Our results show that vaccinated infants, regardless of vaccine strain or regimen, had enhanced myeloid cell responses. However, CD4+T cells were concurrently activated, and the persistence of these activated target cells in oral and/or gastrointestinal tissues may have facilitated oral SIV infection. Immune activation was more pronounced in BCG-vaccinated infant macaques than in AMtb-vaccinated infant macaques, indicating a role for vaccine attenuation. These findings underline the importance of understanding the interplay of vaccine-induced immunity and immune activation and its effect on HIV acquisition risk and outcome in infants.
Convallatoxin-Induced Reduction of Methionine Import Effectively Inhibits Human Cytomegalovirus Infection and Replication
Authors: Cohen Tobias , Williams John D. , Opperman Timothy J. , Sanchez Roberto , Lurain Nell S. , Tortorella Domenico
Published: September 2016

Cytomegalovirus (CMV) is a ubiquitous human pathogen that increases the morbidity and mortality of immunocompromised individuals. The current FDA-approved treatments for CMV infection are intended to be virus specific, yet they have significant adverse side effects, including nephrotoxicity and hematological toxicity. Thus, there is a medical need for safer and more effective CMV therapeutics. Using a high-content screen, we identified the cardiac glycoside convallatoxin as an effective compound that inhibits CMV infection. Using a panel of cardiac glycoside variants, we assessed the structural elements critical for anti-CMV activity by both experimental and
in silico
methods. Analysis of the antiviral effects, toxicities, and pharmacodynamics of different variants of cardiac glycosides identified the mechanism of inhibition as reduction of methionine import, leading to decreased immediate-early gene translation without significant toxicity. Also, convallatoxin was found to dramatically reduce the proliferation of clinical CMV strains, implying that its mechanism of action is an effective strategy to block CMV dissemination. Our study has uncovered the mechanism and structural elements of convallatoxin, which are important for effectively inhibiting CMV infection by targeting the expression of immediate-early genes.

IMPORTANCE
Cytomegalovirus is a highly prevalent virus capable of causing severe disease in certain populations. The current FDA-approved therapeutics all target the same stage of the viral life cycle and induce toxicity and viral resistance. We identified convallatoxin, a novel cell-targeting antiviral that inhibits CMV infection by decreasing the synthesis of viral proteins. At doses low enough for cells to tolerate, convallatoxin was able to inhibit primary isolates of CMV, including those resistant to the anti-CMV drug ganciclovir. In addition to identifying convallatoxin as a novel antiviral, limiting mRNA translation has a dramatic impact on CMV infection and proliferation.
Assessment of the PrP
c
Amino-Terminal Domain in Prion Species Barriers
Authors: Davenport Kristen A. , Henderson Davin M. , Mathiason Candace K. , Hoover Edward A.
Published: September 2016

Chronic wasting disease (CWD) in cervids and bovine spongiform encephalopathy (BSE) in cattle are prion diseases that are caused by the same protein-misfolding mechanism, but they appear to pose different risks to humans. We are interested in understanding the differences between the species barriers of CWD and BSE. We used real-time, quaking-induced conversion (RT-QuIC) to model the central molecular event in prion disease, the templated misfolding of the normal prion protein, PrP
c
, to a pathogenic, amyloid isoform, scrapie prion protein, PrP
Sc
. We examined the role of the PrP
c
amino-terminal domain (N-terminal domain [NTD], amino acids [aa] 23 to 90) in cross-species conversion by comparing the conversion efficiency of various prion seeds in either full-length (aa 23 to 231) or truncated (aa 90 to 231) PrP
c
. We demonstrate that the presence of white-tailed deer and bovine NTDs hindered seeded conversion of PrP
c
, but human and bank vole NTDs did the opposite. Additionally, full-length human and bank vole PrP
c
s were more likely to be converted to amyloid by CWD prions than were their truncated forms. A chimera with replacement of the human NTD by the bovine NTD resembled human PrP
c
. The requirement for an NTD, but not for the specific human sequence, suggests that the NTD interacts with other regions of the human PrP
c
to increase promiscuity. These data contribute to the evidence that, in addition to primary sequence, prion species barriers are controlled by interactions of the substrate NTD with the rest of the substrate PrP
c
molecule.

IMPORTANCE
We demonstrate that the amino-terminal domain of the normal prion protein, PrP
c
, hinders seeded conversion of bovine and white-tailed deer PrP
c
s to the prion forms, but it facilitates conversion of the human and bank vole PrP
c
s to the prion forms. Additionally, we demonstrate that the amino-terminal domain of human and bank vole PrP
c
s requires interaction with the rest of the molecule to facilitate conversion by CWD prions. These data suggest that interactions of the amino-terminal domain with the rest of the PrP
c
molecule play an important role in the susceptibility of humans to CWD prions.
The Cytoskeletal Adaptor Obscurin-Like 1 Interacts with the Human Papillomavirus 16 (HPV16) Capsid Protein L2 and Is Required for HPV16 Endocytosis
Authors: Wüstenhagen Elena , Hampe Laura , Boukhallouk Fatima , Schneider Marc A. , Spoden Gilles A. , Negwer Inka , Koynov Kaloian , Kast W. Martin , Florin Luise
Published: September 2016

The human papillomavirus (HPV) capsid protein L2 is essential for viral entry. To gain a deeper understanding of the role of L2, we searched for novel cellular L2-interacting proteins. A yeast two-hybrid analysis uncovered the actin-depolymerizing factor gelsolin, the membrane glycoprotein dysadherin, the centrosomal protein 68 (Cep68), and the cytoskeletal adaptor protein obscurin-like 1 protein (OBSL1) as putative L2 binding molecules. Pseudovirus (PsV) infection assays identified OBSL1 as a host factor required for gene transduction by three oncogenic human papillomavirus types, HPV16, HPV18, and HPV31. In addition, we detected OBSL1 expression in cervical tissue sections and noted the involvement of OBSL1 during gene transduction of primary keratinocytes by HPV16 PsV. Complex formation of HPV16 L2 with OBSL1 was demonstrated in coimmunofluorescence and coimmunoprecipitation studies after overexpression of L2 or after PsV exposure. We observed a strong colocalization of OBSL1 with HPV16 PsV and tetraspanin CD151 at the plasma membrane, suggesting a role for OBSL1 in viral endocytosis. Indeed, viral entry assays exhibited a reduction of viral endocytosis in OBSL1-depleted cells. Our results suggest OBSL1 as a novel L2-interacting protein and endocytosis factor in HPV infection.

IMPORTANCE
Human papillomaviruses infect mucosal and cutaneous epithelia, and the high-risk HPV types account for 5% of cancer cases worldwide. As recently discovered, HPV entry occurs by a clathrin-, caveolin-, and dynamin-independent endocytosis via tetraspanin-enriched microdomains. At present, the cellular proteins involved in the underlying mechanism of this type of endocytosis are under investigation. In this study, the cytoskeletal adaptor OBSL1 was discovered as a previously unrecognized interaction partner of the minor capsid protein L2 and was identified as a proviral host factor required for HPV16 endocytosis into target cells. The findings of this study advance the understanding of a so far less well-characterized endocytic pathway that is used by oncogenic HPV subtypes.
Tetherin Antagonism by HIV-1 Group M Nef Proteins
Authors: Arias Juan F. , Colomer-Lluch Marta , von Bredow Benjamin , Greene Justin M. , MacDonald Julie , O'Connor David H. , Serra-Moreno Ruth , Evans David T.
Published: September 2016

Although Nef is the viral gene product used by most simian immunodeficiency viruses to overcome restriction by tetherin, this activity was acquired by the Vpu protein of HIV-1 group M due to the absence of sequences in human tetherin that confer susceptibility to Nef. Thus, it is widely accepted that HIV-1 group M uses Vpu instead of Nef to counteract tetherin. Challenging this paradigm, we identified Nef alleles of HIV-1 group M isolates with significant activity against human tetherin. These Nef proteins promoted virus release and tetherin downmodulation from the cell surface and, in the context of
vpu
-deleted HIV-1 recombinants, enhanced virus replication and resistance to antibody-dependent cell-mediated cytotoxicity (ADCC). Further analysis revealed that the Vpu proteins from several of these viruses lack antitetherin activity, suggesting that under certain circumstances, HIV-1 group M Nef may acquire the ability to counteract tetherin to compensate for the loss of this function by Vpu. These observations illustrate the remarkable plasticity of HIV-1 in overcoming restriction by tetherin and challenge the prevailing view that all HIV-1 group M isolates use Vpu to counteract tetherin.

IMPORTANCE
Most viruses of HIV-1 group M, the main group of HIV-1 responsible for the global AIDS pandemic, use their Vpu proteins to overcome restriction by tetherin (BST-2 or CD317), which is a transmembrane protein that inhibits virus release from infected cells. Here we show that the Nef proteins of certain HIV-1 group M isolates can acquire the ability to counteract tetherin. These results challenge the current paradigm that HIV-1 group M exclusively uses Vpu to counteract tetherin and underscore the importance of tetherin antagonism for efficient viral replication.
Multiple Strategies Reveal a Bidentate Interaction between the Nipah Virus Attachment and Fusion Glycoproteins
Authors: Stone Jacquelyn A. , Vemulapati Bhadra M. , Bradel-Tretheway Birgit , Aguilar Hector C.
Published: September 2016

The paramyxoviral family contains many medically important viruses, including measles virus, mumps virus, parainfluenza viruses, respiratory syncytial virus, human metapneumovirus, and the deadly zoonotic henipaviruses Hendra and Nipah virus (NiV). To both enter host cells and spread from cell to cell within infected hosts, the vast majority of paramyxoviruses utilize two viral envelope glycoproteins: the attachment glycoprotein (G, H, or hemagglutinin-neuraminidase [HN]) and the fusion glycoprotein (F). Binding of G/H/HN to a host cell receptor triggers structural changes in G/H/HN that in turn trigger F to undergo a series of conformational changes that result in virus-cell (viral entry) or cell-cell (syncytium formation) membrane fusion. The actual regions of G/H/HN and F that interact during the membrane fusion process remain relatively unknown though it is generally thought that the paramyxoviral G/H/HN stalk region interacts with the F head region. Studies to determine such interactive regions have relied heavily on coimmunoprecipitation approaches, whose limitations include the use of detergents and the micelle-mediated association of proteins. Here, we developed a flow-cytometric strategy capable of detecting membrane protein-protein interactions by interchangeably using the full-length form of G and a soluble form of F, or vice versa. Using both coimmunoprecipitation and flow-cytometric strategies, we found a bidentate interaction between NiV G and F, where both the stalk and head regions of NiV G interact with F. This is a new structural-biological finding for the paramyxoviruses. Additionally, our studies disclosed regions of the NiV G and F glycoproteins dispensable for the G and F interactions.

IMPORTANCE
Nipah virus (NiV) is a zoonotic paramyxovirus that causes high mortality rates in humans, with no approved treatment or vaccine available for human use. Viral entry into host cells relies on two viral envelope glycoproteins: the attachment (G) and fusion (F) glycoproteins. Binding of G to the ephrinB2 or ephrinB3 cell receptors triggers conformational changes in G that in turn cause F to undergo conformational changes that result in virus-host cell membrane fusion and viral entry. It is currently unknown, however, which specific regions of G and F interact during membrane fusion. Past efforts to determine the interacting regions have relied mainly on coimmunoprecipitation, a technique with some pitfalls. We developed a flow-cytometric assay to study membrane protein-protein interactions, and using this assay we report a bidentate interaction whereby both the head and stalk regions of NiV G interact with NiV F, a new finding for the paramyxovirus family.