bluuebunny/crossref_metadata_2025 huggingface dataset:
Investigations on Aerodynamic Loading Limits of Subsonic Compressor Tandem Cascades: End Wall Flow
Authors: Hertel Charlotte , Bode Christoph , Kožulović Dragan , Schneider Tim
Published: September 2014

An optimized subsonic compressor tandem cascade was investigated experimentally and numerically. Since the design aims at applications under incompressible flow conditions, a low inlet Mach number of 0.175 was used. The experiments were carried out at the low speed cascade wind tunnel at the Technische Universität Braunschweig. For the numerical simulations, the CFD-solver TRACE of DLR Cologne was used, together with a curvature corrected k-ω turbulence model and the γ-Reθ transition model. The aerodynamic loading was varied by incidence variation. Results are presented and discussed for different inlet angles: spanwise loss coefficient, turning, pressure rise coefficient and AVR together with contour plots of the wake plane, flow visualization and oil flow pictures. Experimental and numerical results were compared and found to be in good agreement. The secondary flow topology of the front blade is considerably altered by the aerodynamic loading variation, whereas the topology of the rear blade surface is almost unchanged. The effect of the nozzle between the tandem blades, was observable up to the end wall for all investigated incidences. In addition, a comparison is made to published results of previous experimental and numerical investigations of a transonic tandem compressor cascade [1] and its reference single compressor cascade [2]. The comparison of the tandem cascades revealed that the general structures of the secondary flow seem to be similar for similar loading.
Gas-Expanded Lubricant Performance and Effects on Rotor Stability in Turbomachinery
Authors: Weaver Brian K. , Dimond Timothy W. , Kaplan Jason A. , Untaroiu Alexandrina , Clarens Andres F.
Published: September 2014

Gas-expanded lubricants (GELs) are tunable mixtures of synthetic oil and carbon dioxide that enable dynamic control of lubricant viscosity during bearing operation. This control can help reduce bearing power loss and operating temperatures while also providing direct control over bearing stiffness and damping, which can enhance rotordynamic performance. In this work, the bearing and rotordynamic performance of two representative high-speed machines was evaluated when different lubricants, including GELs, were supplied to the machine bearings. The machines chosen for this analysis, an 8-stage centrifugal compressor and a steam turbine-generator system, represent a wide range of speed and loading conditions encountered in modern turbomachinery. The fluids compared for machine performance were standard petroleum-based lubricants, polyol ester synthetic oils, and polyol ester based-GELs. The performance simulations were carried out using a thermoelastohydrodynamic bearing model, which provided bearing stiffness and damping coefficients as inputs to finite element rotordynamic models. Several bearing performance metrics were evaluated including power loss, operating temperature, film thickness, eccentricity, and stiffness and damping coefficients. The rotordynamic analysis included an evaluation of rotor critical speeds, unbalance response, and stability.

Bearing performance results for the compressor showed a 40% reduction in power loss at operating speed when comparing the GEL to the petroleum-based lubricant. The GEL-lubricated compressor also exhibited lower operating temperatures with minimal effects on film thickness. GELs were also predicted to produce lower bearing stiffness when compared to standard fluids in the compressor. Rotordynamic results for the compressor showed that the fluid properties had only minor effects on the unbalance response, while GELs were found to increase the stability margin by 43% when compared with standard fluids. The results from the turbine-generator system also demonstrated increases in low-speed bearing efficiency with the use of GELs, though at higher speeds the onset of turbulent flow in the GEL case offset these efficiency gains. Rotordynamic results for this system showed a contrast with the compressor results, with the GELs producing lower stability margins for a majority of the modes predicted due to increased bearing stiffness in the high-speed turbine bearings and negative stiffness in the lightly loaded, low-speed pinion bearings. These results suggest that GELs could be beneficial in providing control over a wide range of machine designs and operating conditions and that some machines are especially well suited for the tunability that these fluids impart.
Correlation Analysis of Multiple Sensors for Industrial Gas Turbine Compressor Blade Health Monitoring
Authors: Kestner Brian , Hill Chris , Angello Leonard , Barron Josh , Lieuwen Tim
Published: September 2014

This paper summarizes an analysis of data obtained from an instrumented compressor of an operational, heavy duty industrial gas turbine; the goal of the aforementioned analysis is to understand some of the fundamental drivers which may lead to compressor blade vibration. Methodologies are needed to 1.) understand the fundamental drivers of compressor blade vibration, 2.) quantify the severity of “events” which accelerate the likelihood of failure and reduce the remaining life of the blade, and 3.) proactively detect when these issues are occurring so that the operator can take corrective action. The motivation for this analysis lies in understanding the correlations between different sensors which may be used to measure the fundamental drivers and blade vibrations.

In this study, a variety of dynamic data was acquired from an operating engine, including acoustic pressure, bearing vibration, tip timing, and traditional gas path measurements. The acoustic pressure sensors were installed on the first four compressor stages, while the tip timing was installed on the first stage only. These data show the presence of rotating stall instabilities in the front stages of the compressor, occurring during every startup and shutdown, and manifesting itself as increased amplitude oscillations in the dynamic pressure measurements which are manifested in blade and bearing vibrations. The data that lead to these observations were acquired during several startup and shutdown events, and clearly show that the amplitude of these instabilities and the rpm at which they occur can vary substantially.
Test Rig Effect on Performance Measurement for Low Loaded Large Diameter Fan for Automotive Application
Authors: Henner M. , Demory B. , Franquelin F. , Beddadi Y. , Zhang Z.
Published: September 2014

Large diameter fans with low solidity are widely used in automotive application for engine cooling. Their designs with small chord length help reducing the torque on the electrical motor and provide a good aerodynamic compromise between several operating conditions, some of these being at high flow rate. Their global performances are measured according to the ISO standard DP 5801, which allows comparison of results from different facilities. However, some variations in global performances are observed when considering results from two different test rigs. On a fan selected for the purpose of this study, up to 6 % of efficiency is lost on the worst case.

As efficiency is more than ever a key factor to select a component, some experimental and numerical investigations were conducted to analyze the fan behavior on each facility. Two sets of measurement and simulation are performed and compared. Geometries considered for the domain of computation include the test rig plenum, the torquemeter, the ground and a large domain for the atmospheric conditions. The exact fan geometry with tip clearance and under-hub ribs is also considered. Numerical results show in both cases a good agreement with experiment when convergence is reached and for low flow rate when computations are switched to unsteady mode. Comparisons show that simulations are able to capture the different fan behaviors depending on the configuration and those efficiency losses previously observed are correctly predicted.

These results are further analyzed to perform some post-processing. Blade loading remains identical for both cases but disparities appear in the wake and its interaction with the surrounding. Tiny details that are often neglected during experiment and/or simulation appear to be the cause of slight variations. Position of the torquemeter and shape of the plenum are among the parameters that varies and that have cumulative effects. Efficiency being a ration of pressure and torque, variations are rather important.

Finally, these results are discussed in terms of rules for conception and a new geometry less sensible to loss of efficiency is proposed.
Application of Boil Off Gas Compressors in LNG Plants
Authors: Chaker Mustapha , Meher-Homji Cyrus B. , Pillai Pradeep , Bhattacharya Dipanjan , Messersmith David
Published: September 2014

This paper discusses complexities and challenges of managing boil off gas (BOG) in LNG liquefaction plants. Most publications in the past have focused on regasification terminals and have not addressed the area of liquefaction plants. The paper discusses the generation and management of BOG and the associated networks and machinery to manage it. BOG Options available for both greenfield plants and in debottlenecking situations are covered. The advantages and disadvantages of different options and compressor systems are covered and the concept of dynamic simulation as an analysis tool is addressed.
Flat Plate Honeycomb Seals Friction Factor Analysis
Authors: Micio Mirko , Bianchini Cosimo , Massini Daniele , Facchini Bruno , Ceccherini Alberto , Innocenti Luca
Published: September 2014

Among the various type of seals used in gas turbine secondary air system to guarantee sufficient confinement of the main gas path, honeycomb seals well perform in terms of enhanced stability and reduced leakage flow. Due to the large amount of honeycomb cells typically employed in real seals, it is generally convenient to treat the sealing effect of the honeycomb pack as an increased distributed friction factor on the plain top surface. That is why this analysis is focused on a simple configuration composed by a honeycomb facing a flat plate.

In order to evaluate the sealing performance of such honeycomb packs, an experimental campaign was carried out on a stationary test rig where the effects of shaft rotation are neglected. The test rig was designed to analyze different honeycomb geometries so that a large experimental database could be created to correlate the influence of each investigated parameter. Honeycomb seals were varied in terms of hexagonal cell dimension and depth in a range that well represents actual honeycomb packs employed in industrial compressors. For each geometry five different clearances were tested.

This work reports the findings of such experimental campaign whose results were analyzed in order to guide actual seals design and effective estimates of shaft loads. Static pressure measurements reveal that the effects of investigated geometrical parameters on friction factor well correlate with a corrected Mach number based on the cell depth.

The presence of acoustic effects in the seals was further investigated by means of hot wire anemometry. Acoustic forcing due to flow cavity interaction was found to be characterized by a constant Strouhal number based on cell width. Numerical simulations helped in the identification of system eigenmodes and eigenfrequencies providing an explanation to the friction factor enhancement triggered at a certain flow speed.

Finally the generated dataset was tested comparing the predicted leakage flow with experimental data of actual seals (with high pressure and high rotational speed) showing a very good agreement.
Engine Diagnostics in the Eyes of Machine Learning
Authors: Jaw Link C. , Lee Yuh-Jye
Published: September 2014

Machine learning (ML) is a data-driven approach to discovering patterns and knowledge, and it is different from the physics-based approach, which uses the principles of physics to describe a phenomenon. Physics-based approach has dominated the field of engine diagnostics because of the maturity of scientific and engineering knowledge embodied in the design and manufacturing of the engine and its components. Nevertheless, development of ML techniques has accelerated in the last three decades, and the techniques can potentially lower development time and are applicable to a wide variety of industries.

This paper examines some of the most commonly cited ML techniques for handling numerical data and applies them to a gas turbine engine diagnostic problem. The diagnostic problem is to isolate the symptom of engine performance degradations to a root-cause fault or failure. This fault isolation problem is a type of classification problem in the ML world.

A hypothetical engine model for commercial airplanes is used in simulation to create a standard dataset. This dataset is then used by all of the selected techniques. The results from the ML algorithms are evaluated in terms of classification accuracy and misclassification rates.
Investigation of Efficient CFD Methods for Rotating Stall Prediction in a Centrifugal Compressor Stage
Authors: DeMore Daniel , Maghsoudi Elham , Pacheco Jorge , Sorokes James , Hutchinson Brad , Holmes William , Lobo Bryan , Vashistha Vaibhav
Published: September 2014

The Time Transformation Method in ANSYS CFX is investigated as an efficient substitution to Transient Rotor Stator (TRS) analysis for rotating stall prediction in a centrifugal compressor stage. The computational study was performed by varying the number of blade sectors to determine how the circumferential extent of the computational domain affects the accuracy of the stall prediction. The results obtained using a minimum number of blades, approximately one-quarter the full blade count, and approximately one-half the full blade count were compared to both TRS and steady simulations on the same mesh to characterize the predictive capability of each approach. It is shown that both steady and unsteady methods are able to predict the formation of stall cells, but significant qualitative and quantitative differences exist in the flowfield results. The largest mass flow rate at which rotating stall was captured and the number of stall cells were in good agreement with the experimental data.
Synthesis and Analysis of an Independently Controllable Gear Train for Wind Turbines
Authors: Hwang Guan-Shong , Lin Bor-Jeng , Kuang Jao-Hwa , Liao Wei-Hsiang , Perng Jau-Woei , Tsay Der-Min , Wang Wen-Feng
Published: September 2014

The conversion of wind energy into a useful form of electrical power is rapidly and widely becoming popular as an alternative to the usage of fossil fuels. To improve the quality and reliability of a wind turbine, the issue of gear train technology has long been investigated in the continuing development of wind power industry. In this paper, an innovative, independently controllable gear drive that can be used to provide steady output speeds is proposed. With a prototype of this proposed transmission, kinematic/dynamic properties as well as power flow are verified to demonstrate feasibility of this gear system.
Particle Deposition in Internal Cooling Cavities of a Nozzle Guide Vane: Part I — Experimental Investigation
Authors: Clum C. , Bokar E. , Casaday B. , Bons J. P.
Published: September 2014

An experimental facility was fabricated to simulate particle deposition on the internal wall of a nozzle guide vane cooling cavity. The facility supplied particle-laden flow at temperatures up to 540°C to a simplified impingement cooling test section. The heated flow passed through a perforated film hole plate and impacted on the internal surface of a vane wall. The particle-laden impingement jets resulted in the buildup of deposit cones associated with individual impingement jets. The deposit growth rate increased with flow temperature and when the film hole plate temperature was elevated with backside heating. At low temperatures, deposit formed not only as individual cones, but as ridges located at the mid-planes between impinging jets. The base diameter of the deposit structures were found to be larger than the impingement hole diameter due in part to an aerodynamic lensing effect. Further studies using a test piece with optical access were used to document the evolution of deposit cones during continuous deposition.
Particle Deposition in Internal Cooling Cavities of a Nozzle Guide Vane: Part II — Analytical and Computational Modeling
Authors: Casaday B. , Clum C. , Bons J. P.
Published: September 2014

Computational and analytical studies were conducted to investigate particle deposition in the internal film cooling cavities of nozzle guide vanes. Transient deposit growth data were acquired from experimental studies to compare to computational simulations. Particle impact locations were predicted by an Eulerian-Lagrangian particle tracking model and shown to follow analytical trends of aerodynamic lensing. Deposit growth was dominated by the locations of concentrated particle impacts. However, significant deposit growth trends occurred in regions not predicted by the particle tracking model. Simulations were performed to determine if the presence of deposit structures significantly altered subsequent particle trajectories and deposit growth. This effect only moderately improved the comparison with the experiment. The local wall shear was investigated on the deposit surface, and deposit growth was shown to occur in regions of low shear. A shear-based sticking model was developed and applied to computational simulations. The shear-based sticking model qualitatively matched deposit growth trends not observed using several other applied sticking models.
An Experimental Frequency Response Characterization of MEMS Piezoresistive Pressure Transducers
Authors: Hurst Adam M. , Olsen Timothy R. , Goodman Scott , VanDeWeert Joe , Shang Tonghuo
Published: September 2014

Silicon micro-machined piezoresistive based pressure transducers are often used to make high frequency dynamic pressure measurements. The spectral or frequency response of these microelectromechanical systems (MEMS) is a function of the natural resonance of the sensor structure, sensor size, sensor packaging, signal conditioning and transducer mounting in the desired measurement location. The advancement of MEMS micro-fabrication, which has reduced sensor size dramatically, and the high elastic modulus of silicon have allowed the natural resonance of these devices to range from 100kHz to several MHz [1]. As a result, packaging and mounting at the point of measurement are the major factors that determine the flat (0dB) frequency response envelope of the transducer, which is typically quantified by a transfer function. The transfer function quantifies the difference both in magnitude and phase between an input signal and a measured signal in the frequency domain. The dynamic response of pressure transducers has historically been estimated via a unit step input in pressure created through a shock tube test that excites the high natural resonance of the chip. Unfortunately, these tests are less effective at accurately quantifying the frequency response of the transducer in the domain of greatest interest (DC-20kHz), specifically the bandwidth over which the response is flat (0dB). In this work, we present a test methodology using a speaker-driven dynamic pressure calibration setup for experimentally determining the transfer function of a pressure transducer from 1–50kHz. The test setup is validated using capacitive-based microphones with claimed flat spectral characteristics well beyond 50kHz. Using this test setup, we present experimental spectral response results for low-pressure miniature MEMS piezoresistive pressure transducers over the frequency range of 1–50kHz and qualitatively compare these results to traditional shock tube tests. The transducers characterized have been manufactured with several different standard sizes and front-end configurations.
The Effects of Slot Film Cooling on Deposition on a Nozzle Guide Vane
Authors: Prenter Robin , Whitaker Steven M. , Ameri Ali , Bons Jeffrey P.
Published: September 2014

The effects of slot film cooling on deposition in a high pressure nozzle guide vane passage were investigated experimentally and computationally. Experiments were conducted in Ohio State’s Turbine Reaction Flow Rig, using a four-vane cascade, operating at temperatures up to 1353 K. Film cooling was achieved on one of the vanes using a span-wise slot, located at approximately 30% chord on the pressure surface. The coolant’s effect on vane surface temperature was characterized by taking infrared images at various cooling levels. Deposition was produced by injecting sub-bituminous ash particles with a median diameter of 6.48 μm upstream of the vane passage. Several deposition tests were conducted with varying coolant levels. Results exhibit a strong relationship between the coolant flow rate and the amount of ash that deposits on the cooled vane. Capture efficiency was reduced by 70% at the highest coolant flow rate (1.27% of the mass flow rate in the passage). Capture efficiency reduction was compared to that achieved using discrete hole film cooling in other studies. The slot scheme showed similar or larger reductions in capture efficiency at lower coolant mass flow rates. Deposit distribution patterns are affected by regions of cooler temperature, both downstream of the slot where film effects dominate, and slightly upstream of the slot which is cooled by conduction. A computational simulation was conducted to model both the flow and deposition. The solid vane was also discretized to allow for conjugate heat transfer calculations, which produced results that were qualitatively similar to IR measurements, but over predicted the effectiveness of the coolant. An Eulerian-Lagrangian particle tracking model was utilized to track the ash particles through the flow. A sticking model was implemented to determine whether particles stick upon impacting the vane surface, from which deposition rates and distributions are obtained. The computational model under predicted the baseline capture efficiency and the capture efficiency reduction factors for each cooling level, suggesting that the model is not sufficiently sensitive to the temperature changes between tests. Inclusion of surface temperature and local shear dependencies was suggested as an improvement to the sticking model.
Modeling and Analysis of Time-Periodic Gearbox Vibration
Authors: Zhang Shengli , Tang Jiong , Ding Yu
Published: September 2014

In a modern wind turbine, the gearbox is an expensive and fault-prone subsystem. Currently, condition monitoring, based on comparison of data of healthy baseline measurement and online measurement, followed by feature analysis and decision making, is the main approach of diagnosis and prognosis. Although having been employed in many practical implementations, such methods have limitations. For example, a huge database is needed when operating conditions change and normal variations are significant. Traditionally, first-principle-based modeling of gearboxes is considered very challenging, primarily due to their dynamic characteristics that exhibit time-periodicity and encompass a very wide frequency range. In this research, aiming at achieving the predictive modeling capability, a lumped-parameter model of a two-stage laboratory gearbox testbed is constructed based on the assumed mode method. This model can characterize the gearbox dynamic effects including the time-varying mesh stiffness and backlash. The Floquet theory and harmonic balance method are then applied to analytically investigate the system dynamics, where the eigenvalues of the time-periodic gearbox are extracted and correlated to the spectral analysis results of the time-domain response prediction. This modeling approach and the associated analysis lay down a foundation for establishing hybrid dynamic model of complex gearbox systems which will further be utilized in model-based diagnosis and prognosis.
The Droplet Burning Character Influenced by Body Force
Authors: Wang Fang , Jiang Qi , Cui Haoyu
Published: September 2014

Firstly, the influence of centrifugal force generated by rotation on the gas phase is investigated, using a quasi-steady model of one single kerosene and ethanol droplet respectively. The numerical simulations were applied in order to compare the effect of centrifugal force and gravity on the droplet flame. The results show that the influence of centrifugal force is consist with that of the same magnitude gravity force, under the same convection condition. The shape of flame changes obviously when gravity is over 1000g. In addition, experimental apparatus for the evaporation and combustion of single droplet are designed on the basis of previous experiments. The result of simulated evaporation is similar to that of the experimental evaporation. Finally, the evaporation rate, flame temperature and shape of methanol droplet under different gravity field are simulated and compared with each other. The result demonstrates that the evaporation rate, flame shape and temperature are subject to the condition of body force.
Effect of Centrifugal Force on Conventional and Alternative Fuel Surrogate Turbulent Premixed Flames
Authors: Briones Alejandro M. , Sekar Balu , Erdmann Timothy
Published: September 2014

The effect of centrifugal force on flame propagation velocity of stoichiometric propane-, kerosene-, and n-octane-air turbulent premixed flames was numerically examined. The quasi-turbulent numerical model was set in an unsteady two-dimensional geometry with finite length in the transverse and streamwise directions but with infinite length in the spanwise direction. There was relatively good comparison between literature-reported measurements and predictions of propane-air flame propagation velocity as a function of centrifugal force. It was found that for all mixtures the flame propagation velocity increases with centrifugal force. It reaches a maximum then falls off rapidly with further increases in centrifugal force. The results of this numerical study suggest there are no distinct differences among the three mixtures in terms of the effect of centrifugal force on the flame propagation velocity. There are, however, quantitative differences. The numerical models are set in a non-inertial, rotating reference frame. This rotation imposes a radially outward (centrifugal) force. The ignited mixture at one end of the tube raises the temperature and its heat release tends to laminarize the flow. The attained density difference combined with the direction of the centrifugal force promotes Rayleigh-Taylor instability. This instability with thermal expansion and turbulent flame speed constitute the flame propagation mechanism towards the other tube end. A wave is also originated but propagates faster than the flame. During propagation the flame interacts with eddies that wrinkle and/or corrugate the flame. The flame front wrinkles interact with streamtubes that enhance Landau-Darrieus (hydrodynamic) instability, giving rise to a corrugated flame. Under strong stretch conditions the stabilizing equidiffusive-curvature mechanism fails and the flame front breaks up, allowing inflow of unburned mixture into the flame. This phenomenon slows down the flame temporarily and then the flame speeds up faster than before. However, if corrugation is large and the inflow of unburned mixture into the flame is excessive, the latter locally quenches and slows down the flame. This occurs when the centrifugal force is large, tending to blowout the flame. The wave in the tube interacts continuously with the flame through baroclinic torques at the flame front that further enhances the above mentioned flame-eddies interactions. Only at low centrifugal forces the wave intermingles several times with the flame before the averaged flame propagation velocity is determined. The centrifugal force does not substantially increase the turbulent flame speed as commented by previous experimental investigations. The results also suggest that an ultra-compact combustor (UCC) with high-g cavity (HGC) will be limited to centrifugal force levels in the 2000–3000g range.
Unsteady CFD Simulation for High Speed Centrifugal Compressor Operating Near Surge
Authors: Shahin Ibrahim , Gadala Mohamed , Alqaradawi Mohamed , Badr Osama
Published: September 2014

Centrifugal compressor surge and stall are an instabilities flow and system phenomenon, which can lead to a loss of engine power, large pressure transients and, in some cases, failure of the compressor and bearing system. Three-dimensional, compressible, unsteady Navier-Stokes equations are solved, using the sliding mesh at the interface between the moving and stationary parts. The investigated computational domain is composed of inlet pipe, inlet bell, impeller followed by a diffuser. The impeller side cavities are included in the computational domain, to make the simulation more close to the actual case. The present article focuses on the unsteady pressure and velocity results within the impeller and diffuser, at an operating condition close to the surge of the compressor. The computational data compares favorably with the measured data, from literature, for the same compressor and operational point. The pressure fluctuation results are analyzed for the surge and design operating conditions. Through the acquisition of both velocity and transient pressure data, the time evaluation of the unsteady flow during surge is revealed.
Design of PI Controller With Three-Loop Structure for Power Balance of Turboshaft
Authors: Yang Chao , Wang Xi , Liu Mengni , Shi Ruijun , Gao Shihuang
Published: September 2014

Turboshaft control systems are designed to keep the stability of helicopter, which requires that the powerturbine rotor speed remains constant. Furthermore, the power provided by each engine on the same aircraft is probably not equal if the control system provides the same fuel to each one. In this paper, a control loop aiming at balancing engine output torque and load system demand torque was added in the traditional speed-control system. Then a new structure of PI controller was developed with three control loops. Besides, the research showed this control system could be improved to keep the output torque of each engine equal to deal with the different performance degradations of different engines. Finally, the parameters of PI controllers in this control system were achieved by constructing and solving linear matrix inequality constraints based on the theory of regional pole placement for closed-loop system.
Making strong nanomaterials ductile with gradients
Authors: Lu K.
Published: September 2014

Microstructures that increase metal crystallite size from nanoscale with surface depth are both strong and ductile
Pyrimidoindole derivatives are agonists of human hematopoietic stem cell self-renewal
Authors: Fares Iman , Chagraoui Jalila , Gareau Yves , Gingras Stéphane , Ruel Réjean , Mayotte Nadine , Csaszar Elizabeth , Knapp David J. H. F. , Miller Paul , Ngom Mor , Imren Suzan , Roy Denis-Claude , Watts Kori L. , Kiem Hans-Peter , Herrington Robert , Iscove Norman N. , Humphries R. Keith , Eaves Connie J. , Cohen Sandra , Marinier Anne , Zandstra Peter W. , Sauvageau Guy
Published: September 2014

Human adult stem cell expansion

Transfused blood saves lives. Despite the widespread use of this critical resource, it is difficult to increase blood cell numbers outside of the body. By screening thousands of small compounds, Fares
et al.
identify a molecule that expands human stem cell numbers in cord blood. The researchers generate many variations of that molecule and show that one such compound provides even greater human blood cell expansion. If researchers can provide increased numbers of stem cells and progenitor cells, cord blood should find even greater use in the clinic.

Science
, this issue p.
1509
Manipulating spin in organic spintronics
Authors: Bobbert Peter A.
Published: September 2014

Probing the interplay between the electronic and nuclear spins in organic semiconductors

[Also see Report by

Malissa
et al.

]
What's next in 'omics: The metabolome
Authors: Tachibana Chris
Published: September 2014

The youngest sibling in the family of 'omics fields is growing up. Maturing right behind genomics, transcriptomics, and proteomics, metabolomics is the comprehensive analysis of small molecule metabolites. Since most metabolites are generated by enzymatic proteins that result from gene expression, and metabolites give organisms their biochemical characteristics, the metabolome links genotype with phenotype. Metabolomics is still developing, though, as vendors adapt separation and detection instruments to meet its challenges and the research community interprets and integrates the complex data they are acquiring.
Rapid Identification of Positive Blood Cultures by Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry Using Prewarmed Agar Plates
Authors: Bhatti M. M. , Boonlayangoor S. , Beavis K. G. , Tesic V.
Published: September 2014

This study describes an inexpensive and straightforward method for identifying bacteria by matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) directly from positive blood cultures using prewarmed agar plates. Different inoculation methods and incubation times were evaluated to determine the optimal conditions. The two methods using pelleted material from positive culture bottles performed best. In particular, the pellet streak method correctly identified 94% of the Gram negatives following 4 h of incubation and 98% of the Gram positives following 6 h of incubation.
Occurrence of Ochroconis and Verruconis Species in Clinical Specimens from the United States
Authors: Giraldo Alejandra , Sutton Deanna A. , Samerpitak Kittipan , de Hoog G. Sybren , Wiederhold Nathan P. , Guarro Josep , Gené Josepa
Published: September 2014

Ochroconisis a dematiaceous fungus able to infect immunocompetent people. Recently, the taxonomy of the genus has been reevaluated, and the most relevant species,Ochroconis gallopava, was transferred to the new genusVerruconis. Due to the important clinical implications of these fungi and based on the recent classification, it was of interest to know the spectra ofOchroconisandVerruconisspecies in clinical samples received in a reference laboratory in the United States. A set of 51 isolates was identified morphologically and molecularly based on sequence analyses of the nuclear ribosomal RNA (nrRNA), actin, and β-tubulin genes.Verruconis gallopavawas the most common species (68.6%), followed byOchroconis mirabilis(21.5%). One isolate ofOchroconis cordanaewas found, being reported for the first time in a clinical setting. The most common anatomical site of isolation was the lower respiratory tract (58.8%), followed by superficial and deep tissues at similar frequencies (21.6 and 19.6%, respectively). Interestingly, three new species were found, which areOchroconis olivaceaandOchroconis ramosafrom clinical specimens andOchroconis icarusof an environmental origin. Thein vitroantifungal susceptibilities of eight antifungal drugs against theOchroconisisolates revealed that terbinafine and micafungin were the most active drugs.
Analysis of the Evolution and Structure of a Complex Intrahost Viral Population in Chronic Hepatitis C Virus Mapped by Ultradeep Pyrosequencing
Authors: Palmer Brendan A. , Dimitrova Zoya , Skums Pavel , Crosbie Orla , Kenny-Walsh Elizabeth , Fanning Liam J.
Published: September 2014

Hepatitis C virus (HCV) causes chronic infection in up to 50% to 80% of infected individuals. Hypervariable region 1 (HVR1) variability is frequently studied to gain an insight into the mechanisms of HCV adaptation during chronic infection, but the changes to and persistence of HCV subpopulations during intrahost evolution are poorly understood. In this study, we used ultradeep pyrosequencing (UDPS) to map the viral heterogeneity of a single patient over 9.6 years of chronic HCV genotype 4a infection. Informed error correction of the raw UDPS data was performed using a temporally matched clonal data set. The resultant data set reported the detection of low-frequency recombinants throughout the study period, implying that recombination is an active mechanism through which HCV can explore novel sequence space. The data indicate that polyvirus infection of hepatocytes has occurred but that the fitness quotients of recombinant daughter virions are too low for the daughter virions to compete against the parental genomes. The subpopulations of parental genomes contributing to the recombination events highlighted a dynamic virome where subpopulations of variants are in competition. In addition, we provide direct evidence that demonstrates the growth of subdominant populations to dominance in the absence of a detectable humoral response.

IMPORTANCE
Analysis of ultradeep pyrosequencing data sets derived from virus amplicons frequently relies on software tools that are not optimized for amplicon analysis, assume random incorporation of sequencing errors, and are focused on achieving higher specificity at the expense of sensitivity. Such analysis is further complicated by the presence of hypervariable regions. In this study, we made use of a temporally matched reference sequence data set to inform error correction algorithms. Using this methodology, we were able to (i) detect multiple instances of hepatitis C virus intrasubtype recombination at the E1/E2 junction (a phenomenon rarely reported in the literature) and (ii) interrogate the longitudinal quasispecies complexity of the virome. Parallel to the UDPS, isolation of IgG-bound virions was found to coincide with the collapse of specific viral subpopulations.
Effects of Human Anti-Spike Protein Receptor Binding Domain Antibodies on Severe Acute Respiratory Syndrome Coronavirus Neutralization Escape and Fitness
Authors: Sui Jianhua , Deming Meagan , Rockx Barry , Liddington Robert C. , Zhu Quan Karen , Baric Ralph S. , Marasco Wayne A.
Published: September 2014

The receptor binding domain (RBD) of the spike (S) glycoprotein of severe acute respiratory syndrome coronavirus (SARS-CoV) is a major target of protective immunity
in vivo
. Although a large number of neutralizing antibodies (nAbs) have been developed, it remains unclear if a single RBD-targeting nAb or two in combination can prevent neutralization escape and, if not, attenuate viral virulence
in vivo
. In this study, we used a large panel of human nAbs against an epitope that overlaps the interface between the RBD and its receptor, angiotensin-converting enzyme 2 (ACE2), to assess their cross-neutralization activities against a panel of human and zoonotic SARS-CoVs and neutralization escape mutants. We also investigated the neutralization escape profiles of these nAbs and evaluated their effects on receptor binding and virus fitness
in vitro
and in mice. We found that some nAbs had great potency and breadth in neutralizing multiple viral strains, including neutralization escape viruses derived from other nAbs; however, no single nAb or combination of two blocked neutralization escape. Interestingly, in mice the neutralization escape mutant viruses showed either attenuation (Urbani background) or increased virulence (GD03 background) consistent with the different binding affinities between their RBDs and the mouse ACE2. We conclude that using either single nAbs or dual nAb combinations to target a SARS-CoV RBD epitope that shows plasticity may have limitations for preventing neutralization escape during
in vivo
immunotherapy. However, RBD-directed nAbs may be useful for providing broad neutralization and prevention of escape variants when combined with other nAbs that target a second conserved epitope with less plasticity and more structural constraint.

IMPORTANCE
The emergence of severe acute respiratory syndrome coronavirus (SARS-CoV) in 2002 and Middle East respiratory syndrome coronavirus (MERS-CoV) in 2012 has resulted in severe human respiratory disease with high death rates. Their zoonotic origins highlight the likelihood of reemergence or further evolution into novel human coronavirus pathogens. Broadly neutralizing antibodies (nAbs) that prevent infection of related viruses represent an important immunostrategy for combating coronavirus infections; however, for this strategy to succeed, it is essential to uncover nAb-mediated escape pathways and to pioneer strategies that prevent escape. Here, we used SARS-CoV as a research model and examined the escape pathways of broad nAbs that target the receptor binding domain (RBD) of the virus. We found that neither single nAbs nor two nAbs in combination blocked escape. Our results suggest that targeting conserved regions with less plasticity and more structural constraint rather than the SARS-CoV RBD-like region(s) should have broader utility for antibody-based immunotherapy.
Transcriptome Responses of the Host Trichoplusia ni to Infection by the Baculovirus Autographa californica Multiple Nucleopolyhedrovirus
Authors: Chen Yun-Ru , Zhong Silin , Fei Zhangjun , Gao Shan , Zhang Shiying , Li Zhaofei , Wang Ping , Blissard Gary W.
Published: September 2014

Productive infection of
Trichoplusia ni
cells by the baculovirus
Autographa californica
multiple nucleopolyhedrovirus (AcMNPV) leads to expression of ∼156 viral genes and results in dramatic cell remodeling. How the cell transcriptome responds to viral infection was unknown due to the lack of a reference genome and transcriptome for
T. ni
. We used an ∼60-Gb RNA sequencing (RNA-seq) data set from infected and uninfected
T. ni
cells to generate and annotate a
de novo
transcriptome assembly of approximately 70,322
T. ni
unigenes (assembled transcripts), representing the 48-h infection cycle. Using differential gene expression analysis, we found that the majority of host transcripts were downregulated after 6 h postinfection (p.i.) and throughout the remainder of the infection. In contrast, 5.7% (4,028) of the
T. ni
unigenes were upregulated during the early period (0 to 6 h p.i.), followed by a decrease through the remainder of the infection cycle. Also, a small subset of genes related to metabolism and stress response showed a significant elevation of transcript levels at 18 and 24 h p.i. but a decrease thereafter. We also examined the responses of genes belonging to a number of specific pathways of interest, including stress responses, apoptosis, immunity, and protein trafficking. We identified specific pathway members that were upregulated during the early phase of the infection. Combined with the parallel analysis of AcMNPV expression, these results provide both a broad and a detailed view of how baculovirus infection impacts the host cell transcriptome to evade cellular defensive responses, to modify cellular biosynthetic pathways, and to remodel cell structure.

IMPORTANCE
Baculoviruses are insect-specific DNA viruses that are highly pathogenic to their insect hosts. In addition to their use for biological control of certain insects, baculoviruses also serve as viral vectors for numerous biotechnological applications, such as mammalian cell transduction and protein expression for vaccine production. While there is considerable information regarding viral gene expression in infected cells, little is known regarding responses of the host cell to baculovirus infection. In these studies, we assembled a cell transcriptome from the host
Trichoplusia ni
and used that transcriptome to analyze changes in host cell gene expression throughout the infection cycle. The study was performed in parallel with a prior study of changes in viral gene expression. Combined, these studies provide an unprecedented new level of detail and an overview of events in the infection cycle, and they will stimulate new experimental approaches to understand, modify, and utilize baculoviruses for a variety of applications.
Induced Maturation of Human Immunodeficiency Virus
Authors: Mattei Simone , Anders Maria , Konvalinka Jan , Kräusslich Hans-Georg , Briggs John A. G. , Müller Barbara
Published: September 2014

HIV-1 assembles at the plasma membrane of virus-producing cells as an immature, noninfectious particle. Processing of the Gag and Gag-Pol polyproteins by the viral protease (PR) activates the viral enzymes and results in dramatic structural rearrangements within the virion—termed maturation—that are a prerequisite for infectivity. Despite its fundamental importance for viral replication, little is currently known about the regulation of proteolysis and about the dynamics and structural intermediates of maturation. This is due mainly to the fact that HIV-1 release and maturation occur asynchronously both at the level of individual cells and at the level of particle release from a single cell. Here, we report a method to synchronize HIV-1 proteolysis
in vitro
based on protease inhibitor (PI) washout from purified immature virions, thereby temporally uncoupling virus assembly and maturation. Drug washout resulted in the induction of proteolysis with cleavage efficiencies correlating with the off-rate of the respective PR-PI complex. Proteolysis of Gag was nearly complete and yielded the correct products with an optimal half-life (
t
1/2
) of ∼5 h, but viral infectivity was not recovered. Failure to gain infectivity following PI washout may be explained by the observed formation of aberrant viral capsids and/or by pronounced defects in processing of the reverse transcriptase (RT) heterodimer associated with a lack of RT activity. Based on our results, we hypothesize that both the polyprotein processing dynamics and the tight temporal coupling of immature particle assembly and PR activation are essential for correct polyprotein processing and morphological maturation and thus for HIV-1 infectivity.

IMPORTANCE
Cleavage of the Gag and Gag-Pol HIV-1 polyproteins into their functional subunits by the viral protease activates the viral enzymes and causes major structural rearrangements essential for HIV-1 infectivity. This proteolytic maturation occurs concomitant with virus release, and investigation of its dynamics is hampered by the fact that virus populations in tissue culture contain particles at all stages of assembly and maturation. Here, we developed an inhibitor washout strategy to synchronize activation of protease in wild-type virus. We demonstrated that nearly complete Gag processing and resolution of the immature virus architecture are accomplished under optimized conditions. Nevertheless, most of the resulting particles displayed irregular morphologies, Gag-Pol processing was not faithfully reconstituted, and infectivity was not recovered. These data show that HIV-1 maturation is sensitive to the dynamics of processing and also that a tight temporal link between virus assembly and PR activation is required for correct polyprotein processing.