bluuebunny/crossref_metadata_2025 huggingface dataset:
Fatigue Crack Growth Calculations for Vessels Considering Subsurface to Surface Flaw Proximity Rules
Authors: Lacroix Valéry , Hasegawa Kunio , Li Yinsheng
Published: November 2015

If a subsurface flaw is located near a component surface, the subsurface flaw is transformed to a surface flaw in accordance with a subsurface-to-surface flaw proximity rule. The re-characterization process from subsurface to surface flaw is adopted in all fitness-for-service (FFS) codes. However, the specific criteria of the re-characterizations are different among the FFS codes. Recently, the authors have proposed a new subsurface-to-surface flaw proximity rule based on the experiments data and the interaction of stress intensity factors. In this study, extended Finite Element fatigue crack growth calculations were carried out for thick wall component like vessels with subsurface flaws, using the proposed subsurface-to-surface flaw proximity rule and the proximity rule provided in the current ASME Code Section XI.

Different, flaw aspect ratios and ligament distances from subsurface flaws to inner surface of vessel were taken into account. As the results, the current proximity rule and proposed one provide relatively similar fatigue lives, whatever the aspect ratios of the initial subsurface flaws. However, when the thickness of the component decreases this similarity between both proximity rules appears not to be valid anymore.
A Bayesian Statistics Based Design Curve Construction Method for Test Data With Extremely Small Sample Sizes
Authors: Wei Zhigang , Luo Limin , Yang Fulun , Rebandt Robert
Published: November 2015

Fatigue design curve construction is commonly used for durability and reliability assessment of engineering components subjected to cyclic loading. A wide variety of design curve construction methods have been developed over the last decades. Some of the methods have been adopted by engineering codes and widely used in industry. However, the traditional design curve construction methods usually require significant amounts of test data in order for the constructed design curves to be consistently and reliably used in product design and validation. In order to reduce the test sample size and associated testing time and cost, several Bayesian statistics based design curve construction methods have been recently successfully developed by several research groups. Among all of these methods, an efficient Monte Carlo simulation based resampling method developed by the authors of this paper is of particular importance. The method is based on a large amount of reliable historical fatigue test data, the associated probabilistic distributions of the mean and standard deviation of the failure cycles, and an advanced acceptance-rejection resampling algorithm. However, finite element analysis (FEA) methods and a special stress recovery technique are required to process the test data, which is usually a time-consuming process. A more straightforward approach that does not require these intermediate processes is strongly preferred.

This study presents such an approach, in which the only historical information needed is the distribution of the standard deviation of the cycles to failure. The distribution of the mean is directly calculated from the current tested data and the Central Limit Theorem. Neither FEA nor stress recovery technique is required for this approach, and the effort put into design curve construction can be significantly reduced. This method can be used to complement the previously developed Bayesian methods.
Development of Probabilistic Evaluation Models of Fracture Toughness KIc and KIa for Japanese RPV Steels
Authors: Katsuyama Jinya , Katsumata Genshichiro , Onizawa Kunio , Osakabe Kazuya , Yoshimoto Kentaro
Published: November 2015

Probabilistic fracture mechanics (PFM) analysis code PASCAL3 has been developed to apply the PFM analysis to the structural integrity assessment of domestic reactor pressure vessels (RPVs). In this paper, probabilistic evaluation models of fracture toughness KIc and KIa which have the largest scatter among the associated factors based on the database of Japanese RPV steels are presented. We developed probabilistic evaluation models for KIc and KIa based on the Weibull and lognormal distributions, respectively. The models are compared with the existing lower bound of fracture toughness in the Japanese code and probabilistic model in USA. As the results, the 5% confidence limits of the models established in present work corresponded to lower bounds of fracture toughness in the Japanese code. The comparison in the models between present work and USA showed significant differences that may have an influence on fracture probability of RPV.
Laying the Groundwork for a Large-Scale Spent Nuclear Fuel Transportation System
Authors: Feldman Matthew , Connolly Kevin
Published: November 2015

The US Department of Energy Office of Nuclear Energy established the Nuclear Fuels Storage and Transportation Planning Project (NFST) to lay the groundwork for implementing interim storage of commercial spent nuclear fuel (SNF), including associated transportation activities. Progress is being made on long lead time, destination-independent aspects of the SNF transportation system in three areas:

• Institutional: stakeholder interactions needed for system success, including development of a transportation plan, policy development to implement Nuclear Waste Policy Act Section 180(c), and identification of a preliminary suite of national transportation routes based on regulatory requirements and coordination with stakeholders with diverse interests.

• Operational: activities required to run a large-scale transportation system; focus is on development of a new routing analysis tool, study of infrastructure near storage sites that may be de-inventoried first, and development of tools for modeling transportation activities.

• Hardware: casks, railcars, and other items necessary to operate the system. Activities are primarily focused on development of railcars compliant with Association of American Railroads Standard S-2043 and studies on the use of rail casks and their ancillary equipment.

NFST is making significant progress in all of these areas for a future transportation system to transport SNF from commercial reactors.
Block Monitoring Method of SG Tube Support Plate With Intelligent ECT for Maintenance Work
Authors: Noda Masaki , Kobayashi Yuki
Published: November 2015

Intelligent ECT (Eddy Current Testing) probe (I-Probe) has a capability to inspect tubes more productively and more accurately than conventional probes for Steam Generators (SG) as shown in Fig. 1. And I-Probe provides effective “One-Pass” solution by combination with MHI (Mitsubishi Heavy Industries, Ltd.) Intelligent Data Analysis System (MIDAS) [1]. It has been applied to full length tube inspection in Japan since 2003 and there is much field experience to date.

On the other hand, a phenomenon in SG secondary side is known that scale deposits clog holes of quatrefoil type tube support plate (TSP). Water level oscillation of secondary side caused by excessive blockage of scale deposits may decrease operation efficiency and it can be a cause of unintended troubles. Therefore, periodical monitoring of blockage condition and applying countermeasures like secondary side cleaning are very important. A new method has been developed to evaluate blockage condition of every TSP around all tubes automatically using I-Probe data. Also, a new software has been developed to visualize the evaluation results as color maps.

This new method may contribute to increase the reliability of SG maintenance like cleaning, because the new method makes it possible to monitor a whole SG condition more precisely.
Standardized Through-Wall Distributions of Dissimilar Metal Weld Residual Stress
Authors: Broussard John E.
Published: November 2015

The residual stresses imparted by the welding process are a principal factor in the process of primary water stress corrosion cracking (PWSCC) of Alloy 82/182 nickel-alloy (i.e., dissimilar metal or DM) piping butt welds in PWRs. While Section XI of the ASME Code requires that residual stresses are considered in crack growth calculations, there is little guidance or requirement on how to calculate them. Analytical models are frequently used to simulate the welding process in order to predict the residual stress distribution in the weld and base material as an input to crack growth calculations. The crack growth calculations, in turn, have demonstrated a high sensitivity to the welding residual stress distribution inputs.

While significant progress has been made in understanding and reducing the variability in calculated residual stress among modelers as well as the variability in measured residual stress among different techniques, there remains some uncertainty regarding any given measured or calculated distribution. A feasible alternative to calculating through-wall stress distributions with analytical models on a case-by-case basis is to develop a set of standardized through-wall stress distributions that are applicable to DM welds. Examples of standardized through-wall distributions for residual stress are found in numerous consensus code and standards. The benefit of established through-wall stress distributions is that evaluations for flaws in welds would start from a uniform basis on one of the key inputs to the crack growth calculation, reducing the time required to perform and review flaw evaluations.

This paper presents and describes the technical basis for a set of through-wall distributions for common DM welds found in the US nuclear industry. The basis of the distributions include the results of analytical models, including uncertainty, as well as measured data for through-wall stress in DM welds.
Large EDF Tests on Aged Cast Duplex Stainless Steel Components: Part I — Reduced Scale Tests
Authors: Le Delliou Patrick , Saillet Sébastien , Bezdikian Georges
Published: November 2015

Thermal ageing of cast duplex stainless steel primary loops components (elbows, pump casings and branch connections) is a concern for long-term operation of EDF nuclear power plants. The thermal ageing embrittlement results from the micro-structural evolution of the ferrite phase (spinodal decomposition), and can reduce the fracture toughness properties of the steel. In addition, it is necessary to consider manufacturing quality and the possible occurrence of casting defects such as shrinkage cavities. In a context of life extension, it is important to assess the safety margins to crack initiation and crack propagation instability.

This paper presents several tests conducted by EDF on aged cast duplex stainless steel NPP components, respectively on two-third scale elbows and welded mock-ups. The main characteristics of the tests are recalled, the results are presented, and finally, the lessons drawn are summarized.

These tests and their detailed analyses contribute to validate and justify the methodology used by EDF in the integrity assessment of in-service cast duplex stainless steel components.
Assessing the Impact of ASME B31.3 2012 Fatigue Rule Changes on High Strength Piping
Authors: Brown Warren
Published: November 2015

The 2012 edition of ASME B31.3 Process Piping Code [1] included an update to the fatigue assessment rules which limited the allowable stress value used in the fatigue assessment to 138 MPa (20 ksi). This change was made due to the knowledge that higher strength materials, especially those materials with yield strength to tensile strength ratios above 0.8, do not tend to exhibit significantly longer fatigue life as compared to lower strength materials. This change means that for existing high-strength piping in plants that were designed using pre-2012 B31.3 [2] and are in fatigue service, the end-user must now recalculate the piping remaining life based on new requirements. Depending on the size of the plant under consideration and the level of high-strength piping used, such a recalculation may be an extensive scope of work.

This paper uses a comparison between the rules in ASME B31.3 and the fatigue life prediction methods outlined in API RP 579-1 / ASME FFS-1 [3] in order to establish a categorization methodology which is used to identify which pre-2012 high strength piping systems will require re-assessment, more frequent monitoring and/or may have a shorter than anticipated life than the original design basis. The methodology allows for easy categorization of the piping systems to allow efforts to be focused on the most appropriate piping systems. The need for this work came from concerns regarding the extensive use of Duplex Stainless Steel piping on a large offshore platform that was designed prior to ASME B31.3 2012.
The Significance of the Tertiary Creep Criterion in Setting Time-Dependent Allowable Stresses
Authors: Swindeman Robert , Ren Weiju , Swindeman Michael J.
Published: November 2015

The database for Alloy 800H was reviewed with respect to the initiation of tertiary creep and subsequent rupture. Data covered temperatures in the range of 600 to 1000°C and times to 100,000 hours. The establishment of the time to initiate tertiary creep presented a problem because of the non-classical behavior of creep often exhibited in the creep curves. Stress values based on the current tertiary creep and rupture criteria were compared for several heats of material considering both classical and non-classical creep data. Fits to tertiary creep showed more scatter and it was found that 80% of the minimum stress for tertiary creep was generally lower than 67% of the minimum stress to rupture. Using only data from classical curves did produce stress values higher than those from the rupture criterion.
Fracture Protection of CANDU Zr-2.5Nb Pressure Tubes With High Hydrogen Equivalent Concentration
Authors: Doddihal Preeti , Scarth Douglas , Mosbrucker Paula , Xu Steven
Published: November 2015

The core of a CANDU®1 (CANada Deuterium Uranium) pressurized heavy water reactor includes horizontal Zr-2.5Nb alloy pressure tubes that contain the fuel. Pressure-temperature limits are used in CANDU® reactors for normal operation heat-up and cool-down conditions to maintain margins against fracture. The pressure-temperature limits are determined by postulating a 20 mm long axial through-wall crack in the pressure tube and using a fracture toughness-based calculation procedure. Due to a corrosion reaction with the heavy water coolant, pressure tubes absorb deuterium isotope in service, resulting in an increase in hydrogen equivalent concentration. Experiments have shown that high hydrogen equivalent concentration reduces the fracture toughness of pressure tube material at low temperatures during reactor heat-up and cool-down from normal operating temperatures. New fracture toughness curves that are applicable to material with high hydrogen equivalent concentration have been developed to address this issue. These curves are being used to develop new pressure-temperature limits for fracture protection of CANDU® pressure tubes. The methodology for deriving the pressure-temperature limits for a CANDU® Zr-2.5Nb pressure tube using the new fracture toughness curves is presented in this paper. Preliminary results of pressure-temperature limits for a CANDU® reactor are also provided.
“Live” Repair of Gas Pipeline With Deep Girth Weld Crack
Authors: Tronskar Jens P. , Törnqvist Rikard , Guan Ong Hock , Bruce William A.
Published: November 2015

In-line inspection (ILI) of the main 48” × 21 mm wall thickness API 5L grade X70 export gas pipeline of an offshore oil and gas production field was performed. The ILI using a high resolution Magnetic Flux Leak (MFL) pig revealed an anomaly in a girth weld in the onshore portion of the pipeline. A dig campaign was organized to carry out detailed inspection and sizing of the detected anomaly by external Phased Array Ultrasonic Testing (PAUT) and Time of Flight Diffraction (TOFD). The inspection confirmed the presence of a deep external, surface breaking, girth weld crack. The presence of the defect raised concern for the integrity of the pipeline and it was a question if it was necessary to shut the line down for immediate repair or if repair could be performed at a later date.

CTOD fracture toughness testing was performed on a reproduced girth weld. The joint tested was welded using pipe remaining from installation with virtually identical chemistry and mechanical properties as the pipes joined at the cracked girth weld location according to the mill certificates. For the welding, the same welding consumables, original WPS, and the welding system (CRC-Evans system using internal line up clamp and root pass) were used.

Based on the fracture mechanics test results and the analyses performed, it was recommended to repair the pipeline as soon as practical. It was decided to repair the cracked girth weld using a full encirclement snug fitting (Type -B), welded split sleeve according to the PRCI Repair Manual. To assess the risk of welding the split sleeve onto the “live” pipe, which could increase the crack driving force due to the thermal stresses from welding and preheating, a combined 3D non-linear thermal and fracture mechanics FEA modelling of the girth weld crack and thermal distributions were performed in Abaqus. As for all welding onto “live” pipelines, the overall risk associated with burn-through and hydrogen induced heat-affected zone cracking (HAZ) was also assessed.

This paper describes the methodology applied for the assessment and qualification of the repair and the analysis of the thermal, operating and residual stresses on the crack driving force to establish if the repair operation was safe to undertake.
Analytic estimation and minimization of line edge roughness in electron-beam lithography
Authors: Guo Rui , Lee Soo-Young , Choi Jin , Park Sung-Hoon , Shin In-Kyun , Jeon Chan-Uk
Published: November 2015

As the feature size is reduced well below 100 nm, the line edge roughness (LER) will eventually become a resolution-limiting factor in the electron-beam (e-beam) lithography since the LER does not scale with the feature size. Therefore, it is essential to minimize the LER in order to achieve the highest resolution possible by the e-beam lithographic process. A simulation or experiment based method for minimizing the LER can be very time-consuming and expensive since repetitive simulations or experiments may be required. In this study, a new analytic model and a method for estimating the LER are developed based on the model, and an analytic procedure for minimizing the LER is also derived based on the new analytic model. In this new approach, the LER is derived from the distribution of the stochastic developing rate in the resist, which is assumed to be known. The results obtained by the analytic estimation method and the minimization procedure are shown to be close to those by the simulation method. The current work includes generalization of the results of this study with more practical models.
Investigation of auditory distance perception and preferences in concert halls by using virtual acoustics
Authors: Kuusinen Antti , Lokki Tapio
Published: November 2015

Virtual acoustics with multichannel sound reproduction was used to study auditory distance perception in four concert halls with multiple sound sources on stage. Eight subjects reported apparent auditory distances in five seating positions from 10 to 26 m to the middle of the sources on stage. The distance estimates were collected by absolute distance estimation procedure as well as a free modulus estimation procedure including both within and between halls evaluations. In addition, pairwise preferences were collected for two positions within each hall and for one position between halls. Results reveal that the perception of distance is dependent on the hall acoustics and show how the strength factor G and direct-to-reverberant energy ratio covary in relation to perceptual distances in these halls. The results also indicate that in such large spaces the overestimation of short distances may continue up to and further than 10 m from the sound sources. Preference results show that closer seats were liked more than further ones and that the strength of this preference is associated with the difference in perceptual distances.
Reconstruction of an acoustic pressure field in a resonance tube by particle image velocimetry
Authors: Kuzuu K. , Hasegawa S.
Published: November 2015

A technique for estimating an acoustic field in a resonance tube is suggested. The estimation of an acoustic field in a resonance tube is important for the development of the thermoacoustic engine, and can be conducted employing two sensors to measure pressure. While this measurement technique is known as the two-sensor method, care needs to be taken with the location of pressure sensors when conducting pressure measurements. In the present study, particle image velocimetry (PIV) is employed instead of a pressure measurement by a sensor, and two-dimensional velocity vector images are extracted as sequential data from only a one- time recording made by a video camera of PIV. The spatial velocity amplitude is obtained from those images, and a pressure distribution is calculated from velocity amplitudes at two points by extending the equations derived for the two-sensor method. By means of this method, problems relating to the locations and calibrations of multiple pressure sensors are avoided. Furthermore, to verify the accuracy of the present method, the experiments are conducted employing the conventional two-sensor method and laser Doppler velocimetry (LDV). Then, results by the proposed method are compared with those obtained with the two-sensor method and LDV.
The Effects of Slackline Balance Training on Postural Control in Older Adults
Authors: Thomas Monika , Kalicinski Michael
Published: November 2015

The present study investigated whether slackline training enhances postural control in older adults. Twenty-four participants were randomized into an intervention and a control group. The intervention group received 6 weeks of slackline training, two times per week. Pre–post measurement included the time of different standing positions on a balance platform with and without an external disturbance and the acceleration of the balance platform. Results showed significantly improved standing times during one-leg stance without external disturbance and a significantly reduced acceleration of the balance platform for the intervention group after the training period during tandem stance with and without an external disturbance. We conclude that slackline training in older adults has a positive impact on postural control and thus on the reduction of fall risk.
Tweeting the Lecture: How Social Media Can Increase Student Engagement in Higher Education
Authors: Scott Olan Kees Martin , Stanway Alicia R.
Published: November 2015

The higher education sector increasingly uses social media as an educational tool to develop a sense of community and foster student engagement, particularly as social networking sites have become an integral part of the lives of digital natives. The current study sought to explore whether the use of Twitter could foster student engagement in a sport marketing course, specifically by embedding Twitter through two assessments, online lectures and weekly tasks. Mean score comparisons indicated that over a 13-week semester, students (N = 68) felt more engaged and included in the course because it had Twitter, found Twitter to be relatively easy to use, and the use of social media aligned with course objectives. The results of the current study have salience in sport management education, because the effective use of Twitter within a higher education context demonstrates how the use of social media can foster engagement with course materials.
LISA Pathfinder tests spacetime sensor
Authors: Clery Daniel
Published: November 2015

A European space probe is set to pave the way for measurements of gravitational waves.
A faster, brighter picture of brain cells in action
Authors: Underwood Emily
Published: November 2015

New voltage-sensor achieves submillisecond precision.
Humans may have reached Chile by 18,500 years ago
Authors: Gibbons Ann
Published: November 2015

Monte Verde stone tools may be the oldest in the Americas.
Transport: A roadblock to climate change mitigation?
Authors: Creutzig Felix , Jochem Patrick , Edelenbosch Oreane Y. , Mattauch Linus , Vuuren Detlef P. van , McCollum David , Minx Jan
Published: November 2015

Urban mobility solutions foster climate mitigation
Nonparadoxical evolutionary stability of the recombination initiation landscape in yeast
Authors: Lam Isabel , Keeney Scott
Published: November 2015

Recombination: The birds and the yeast

Apes and mice have a specific gene,
PRDM9
, that is associated with genomic regions with high rates of recombination, called hotspots. In species with
PRDM9
, hotspots move rapidly within the genome, varying among populations and closely related species (see the Perspective by Lichten). To investigate recombination hotspots in species lacking
PRDM9
, Singhal
et al.
examined bird genomes, which lack a
PRDM9
gene. They looked closely at the genomes of finch species and found that recombination was localized to the promoter regions of genes and highly conserved over millions of years. Similarly, Lam and Keeney examined recombination localization within yeast, which also lacks
PRDM9
. They found a similar more-or-less fixed pattern of hotspots. Thus, recombination in species lacking a
PRDM9
gene shows similar patterns of hotspot localization and evolution.

Science
, this issue p.
913
, p.
928
; see also p.
932
Operational redundancy in axon guidance through the multifunctional receptor Robo3 and its ligand NELL2
Authors: Jaworski Alexander , Tom Irene , Tong Raymond K. , Gildea Holly K. , Koch Alexander W. , Gonzalez Lino C. , Tessier-Lavigne Marc
Published: November 2015

No going back

The mammalian spinal cord coordinates neuronal systems across the body. Axons that cross the spinal cord midline during development first need permission to cross and then instruction not to keep crossing back and forth. Jaworski
et al.
studied the axonal guidance receptor ROBO3 and found a ligand NELL2 in mice that appears to help in this process.

Science
, this issue p.
961
Open-ocean fish reveal an omnidirectional solution to camouflage in polarized environments
Authors: Brady Parrish C. , Gilerson Alexander A. , Kattawar George W. , Sullivan James M. , Twardowski Michael S. , Dierssen Heidi M. , Gao Meng , Travis Kort , Etheredge Robert Ian , Tonizzo Alberto , Ibrahim Amir , Carrizo Carlos , Gu Yalong , Russell Brandon J. , Mislinski Kathryn , Zhao Shulei , Cummings Molly E.
Published: November 2015

Disappearing act

Unlike coastal regions and reefs, the open ocean is mostly empty. Many fish species, nonetheless, spend most of their lives there. Such emptiness makes camouflage exceedingly difficult, so how does an organism hide in water filled with bouncing and reflected light? Brady
et al.
show that some families of fish have evolved skin that reflects and polarizes light, allowing them to blend into their mirrorlike conditions more easily. These results help to explain the silvery coloration found in sea-living fish across the world's oceans.

Science
, this issue p.
965
Putting the breaks on meiosis
Authors: Lichten Michael
Published: November 2015

Yeast and birds reveal remarkable evolutionary stability in recombination patterns

[Also see Research Articles by

Singhal
et al.

and
Lam and Keeney
]
Opening the window for aqueous electrolytes
Authors: Smith Leland , Dunn Bruce
Published: November 2015

Lithium batteries can operate with a safer “water-in-salt” electrolyte

[Also see Research Article by

Suo
et al.

]
Restoring voice
Authors: Long Jennifer L. , Chhetri Dinesh K.
Published: November 2015

Engineered vocal cords could soon replace damaged tissue
America's science legacy
Authors: deGrasse Tyson Neil
Published: November 2015

In 1863, U.S. President Abraham Lincoln delivered his now famous Gettysburg Address on the open field of that bloody Civil War battle. Not many speeches by political leaders get remembered beyond the moment. Even fewer ever get cut into stone. In this case, of course, both are true. We know the words. We recite passages from it. And, in its entirety, the speech graces a wall of the Lincoln Memorial in Washington, DC.
Blood Transcriptional Biomarkers for Active Tuberculosis among Patients in the United States: a Case-Control Study with Systematic Cross-Classifier Evaluation
Authors: Walter Nicholas D. , Miller Mikaela A. , Vasquez Joshua , Weiner Marc , Chapman Adam , Engle Melissa , Higgins Michael , Quinones Amy M. , Rosselli Vanessa , Canono Elizabeth , Yoon Christina , Cattamanchi Adithya , Davis J. Lucian , Phang Tzu , Stearman Robert S. , Datta Gargi , Garcia Benjamin J. , Daley Charles L. , Strong Michael , Kechris Katerina , Fingerlin Tasha E. , Reves Randall , Geraci Mark W.
Published: November 2015

Blood transcriptional signatures are promising for tuberculosis (TB) diagnosis but have not been evaluated among U.S. patients. To be used clinically, transcriptional classifiers need reproducible accuracy in diverse populations that vary in genetic composition, disease spectrum and severity, and comorbidities. In a prospective case-control study, we identified novel transcriptional classifiers for active TB among U.S. patients and systematically compared their accuracy to classifiers from published studies. Blood samples from HIV-uninfected U.S. adults with active TB, pneumonia, or latent TB infection underwent whole-transcriptome microarray. We used support vector machines to classify disease state based on transcriptional patterns. We externally validated our classifiers using data from sub-Saharan African cohorts and evaluated previously published transcriptional classifiers in our population. Our classifier distinguishing active TB from pneumonia had an area under the concentration-time curve (AUC) of 96.5% (95.4% to 97.6%) among U.S. patients, but the AUC was lower (90.6% [89.6% to 91.7%]) in HIV-uninfected Sub-Saharan Africans. Previously published comparable classifiers had AUC values of 90.0% (87.7% to 92.3%) and 82.9% (80.8% to 85.1%) when tested in U.S. patients. Our classifier distinguishing active TB from latent TB had AUC values of 95.9% (95.2% to 96.6%) among U.S. patients and 95.3% (94.7% to 96.0%) among Sub-Saharan Africans. Previously published comparable classifiers had AUC values of 98.0% (97.4% to 98.7%) and 94.8% (92.9% to 96.8%) when tested in U.S. patients. Blood transcriptional classifiers accurately detected active TB among U.S. adults. The accuracy of classifiers for active TB versus that of other diseases decreased when tested in new populations with different disease controls, suggesting additional studies are required to enhance generalizability. Classifiers that distinguish active TB from latent TB are accurate and generalizable across populations and can be explored as screening assays.
Evaluation of the BD Max Enteric Parasite Panel for Clinical Diagnostics
Authors: Mölling Paula , Nilsson Peter , Ennefors Theresa , Ögren Jessica , Florén Kerstin , Thulin Hedberg Sara , Sundqvist Martin
Published: November 2015

We compared the performance of the BD Max enteric parasite panel to routine microscopy and an in-house PCR for the detection of
Giardia intestinalis
,
Entamoeba histolytica
, and
Cryptosporidium
spp. The enteric parasite panel showed good specificity for all targets and good sensitivity for
E. histolytica
and
Cryptosporidium
spp. Sensitivity for
G. intestinalis
with the BD Max enteric parasite panel was equivalent to that with microscopy.
Evaluation of an Image Analysis Device (APAS) for Screening Urine Cultures
Authors: Glasson John , Hill Rhys , Summerford Michael , Giglio Steven
Published: November 2015

While advancements have been made in some areas of pathology with diagnostic materials being screened using image analysis technologies, the reporting of cultures from agar plates remains a manual process. We compared the results for 2,163 urine cultures read by a reference panel of microbiologists, by the routine laboratory process, and by an automated plate reading system, APAS (LBT Innovations Ltd., South Australia). APAS detected colonies with a sensitivity of 99.1% and a specificity of 99.3% on blood agar, while on MacConkey agar, the colony detection sensitivity was 99.4% with a specificity of 99.3%. The device's ability to enumerate growth had an accuracy of 89.2%, and the morphological identification of colonies showed a high level of performance for the colony types typical of
Escherichia coli
and other enteric bacilli. On blood agar, lactose-fermenting colonies were morphologically identified with a sensitivity of 98.9%, while on MacConkey agar they were identified with a sensitivity of 99.2%. In this first clinical evaluation, APAS demonstrated high performance in the detection, enumeration, and colony classification of isolates compared with that for conventional plate-reading methods. The device found all cases reported by the laboratory and detected the most commonly encountered organisms found in urinary tract infections.
Comparative Study of a Novel Biochemical Assay, the Rapidec Carba NP Test, for Detecting Carbapenemase-Producing Enterobacteriaceae
Authors: Lifshitz Ziv , Adler Amos , Carmeli Yehuda
Published: November 2015

The novel biochemical test, the Rapidec Carba NP (RCNP), was evaluated using carbapenemase- and non-carbapenemase-producing
Enterobacteriaceae
isolates. The RCNP test was compared with the Carba NP test (CNP) and the modified Hodge test. Compared to the CNP test, the RCNP test had identical sensitivity (96%) and lower specificity (93% versus 100%). The medium used to culture the isolates significantly affected test sensitivity and specificity. The RCNP test was quicker and easier to perform than the other tests.
A Simple and Safe Protocol for Preparing Brucella Samples for Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry Analysis
Authors: Mesureur Jennifer , Ranaldi Sébastien , Monnin Valérie , Girard Victoria , Arend Sandrine , Welker Martin , O'Callaghan David , Lavigne Jean-Philippe , Keriel Anne
Published: November 2015

We describe a simple protocol to inactivate the biosafety level 3 (BSL3) pathogens
Brucella
prior to their analysis by matrix-assisted laser desorption ionization–time of flight mass spectrometry. This method is also effective for several other bacterial pathogens and allows storage, and eventually shipping, of inactivated samples; therefore, it might be routinely applied to unidentified bacteria, for the safety of laboratory workers.
Commentary: Unveiling New Aspects of Meningococcal Carriage and Disease Prevention
Authors: Gottfredsson Magnus
Published: November 2015

Recently, two protein-based vaccines have been approved for the prevention of invasive meningococcal disease caused by
Neisseria meningitidis
serogroup B (MenB). It is therefore important to study carefully if and how these pathogens respond to widespread vaccination. Traditionally, meningococci have been classified on the basis of capsular phenotypes, but variable levels of capsule expression can influence the results, mainly among MenB strains. In this issue, Jones and colleagues (J Clin Microbiol 54:25–34, 2016,
http://dx.doi.org/10.1128/JCM.01447-15
) compare whole-genome sequencing to traditional phenotypic methods of classifying meningococci. They demonstrate that for MenB in particular, sequencing-based methods are far superior to traditional methods, especially when it comes to characterizing carriage isolates. This has important implications for future surveillance.
Engineering Enhanced Vaccine Cell Lines To Eradicate Vaccine-Preventable Diseases: the Polio End Game
Authors: van der Sanden Sabine M. G. , Wu Weilin , Dybdahl-Sissoko Naomi , Weldon William C. , Brooks Paula , O'Donnell Jason , Jones Les P. , Brown Cedric , Tompkins S. Mark , Oberste M. Steven , Karpilow Jon , Tripp Ralph A.
Published: November 2015

Vaccine manufacturing costs prevent a significant portion of the world's population from accessing protection from vaccine-preventable diseases. To enhance vaccine production at reduced costs, a genome-wide RNA interference (RNAi) screen was performed to identify gene knockdown events that enhanced poliovirus replication. Primary screen hits were validated in a Vero vaccine manufacturing cell line using attenuated and wild-type poliovirus strains. Multiple single and dual gene silencing events increased poliovirus titers >20-fold and >50-fold, respectively. Host gene knockdown events did not affect virus antigenicity, and clustered regularly interspaced short palindromic repeat (CRISPR)-Cas9-mediated knockout of the top candidates dramatically improved viral vaccine strain production. Interestingly, silencing of several genes that enhanced poliovirus replication also enhanced replication of enterovirus 71, a clinically relevant virus to which vaccines are being targeted. The discovery that host gene modulation can markedly increase virus vaccine production dramatically alters mammalian cell-based vaccine manufacturing possibilities and should facilitate polio eradication using the inactivated poliovirus vaccine.

IMPORTANCE
Using a genome-wide RNAi screen, a collection of host virus resistance genes was identified that, upon silencing, increased poliovirus and enterovirus 71 production by from 10-fold to >50-fold in a Vero vaccine manufacturing cell line. This report provides novel insights into enterovirus-host interactions and describes an approach to developing the next generation of vaccine manufacturing through engineered vaccine cell lines. The results show that specific gene silencing and knockout events can enhance viral titers of both attenuated (Sabin strain) and wild-type polioviruses, a finding that should greatly facilitate global implementation of inactivated polio vaccine as well as further reduce costs for live-attenuated oral polio vaccines. This work describes a platform-enabling technology applicable to most vaccine-preventable diseases.
Three-Dimensional Structural Characterization of HIV-1 Tethered to Human Cells
Authors: Strauss Joshua D. , Hammonds Jason E. , Yi Hong , Ding Lingmei , Spearman Paul , Wright Elizabeth R.
Published: November 2015

Tetherin (BST2, CD317, or HM1.24) is a host cellular restriction factor that prevents the release of enveloped viruses by mechanically linking virions to the plasma membrane. The precise arrangement of tetherin molecules at the plasma membrane site of HIV-1 assembly, budding, and restriction is not well understood. To gain insight into the biophysical mechanism underlying tetherin-mediated restriction of HIV-1, we utilized cryo-electron tomography (cryo-ET) to directly visualize HIV-1 virus-like particles (VLPs) and virions tethered to human cells in three dimensions (3D). Rod-like densities that we refer to as tethers were seen connecting HIV-1 virions to each other and to the plasma membrane. Native immunogold labeling showed tetherin molecules located on HIV-1 VLPs and virions in positions similar to those of the densities observed by cryo-ET. The location of the tethers with respect to the ordered immature Gag lattice or mature conical core was random. However, tethers were not uniformly distributed on the viral membrane but rather formed clusters at sites of contact with the cell or other virions. Chains of tethered HIV-1 virions often were arranged in a linear fashion, primarily as single chains and, to a lesser degree, as branched chains. Distance measurements support the extended tetherin model, in which the coiled-coil ectodomains are oriented perpendicular with respect to the viral and plasma membranes.

IMPORTANCE
Tetherin is a cellular factor that restricts HIV-1 release by directly cross-linking the virus to the host cell plasma membrane. We used cryo-electron tomography to visualize HIV-1 tethered to human cells in 3D. We determined that tetherin-restricted HIV-1 virions were physically connected to each other or to the plasma membrane by filamentous tethers that resembled rods ∼15 nm in length, which is consistent with the extended tetherin model. In addition, we found the position of the tethers to be arbitrary relative to the ordered immature Gag lattice or the mature conical cores. However, when present as multiple copies, the tethers clustered at the interface between virions. Tethered HIV-1 virions were arranged in a linear fashion, with the majority as single chains. This study advances our understanding of tetherin-mediated HIV-1 restriction by defining the spatial arrangement and orientation of tetherin molecules at sites of HIV-1 restriction.
Origin of Rebound Plasma HIV Includes Cells with Identical Proviruses That Are Transcriptionally Active before Stopping of Antiretroviral Therapy
Authors: Kearney Mary F. , Wiegand Ann , Shao Wei , Coffin John M. , Mellors John W. , Lederman Michael , Gandhi Rajesh T. , Keele Brandon F. , Li Jonathan Z.
Published: November 2015

Understanding the origin of HIV variants during viral rebound may provide insight into the composition of the HIV reservoir and has implications for the design of curative interventions. HIV single-genome sequences were obtained from 10 AIDS Clinical Trials Group participants who underwent analytic antiretroviral therapy (ART) interruption (ATI). Rebounding variants were compared with those in pre-ART plasma in all 10 participants and with on-ART peripheral blood mononuclear cell (PBMC)-associated DNA and RNA (CA-RNA) in 7/10 participants. The highest viral diversities were found in the DNA and CA-RNA populations. In 3 of 7 participants, we detected multiple, identical DNA and CA-RNA sequences during suppression on ART that exactly matched plasma HIV sequences. Hypermutated DNA and CA-RNA were detected in four participants, contributing to diversities in these compartments that were higher than in the pre-ART and post-ATI plasma. Shifts in the viral rebound populations could be detected in some participants over the 2- to 3-month observation period. These findings suggest that a source of initial rebound viremia could be populations of infected cells that clonally expanded prior to and/or during ART, some of which were already expressing HIV RNA before treatment was interrupted. These clonally expanding populations of HIV-infected cells may represent an important target for strategies aimed at achieving reservoir reduction and sustained virologic remission.

IMPORTANCE
Antiretroviral therapy alone cannot eradicate the HIV reservoir, and viral rebound is generally rapid after treatment interruption. It has been suggested that clonal expansion of HIV-infected cells is an important mechanism of HIV reservoir persistence, but the contribution of these clonally proliferating cells to the rebounding virus is unknown. We report a study of AIDS Clinical Trials Group participants who underwent treatment interruption and compared rebounding plasma virus with that found within cells prior to treatment interruption. We found several incidences in which plasma HIV variants exactly matched that of multiple proviral DNA copies from infected blood cells sampled before treatment interruption. In addition, we found that these cells were not dormant but were generating unspliced RNA transcripts before treatment was interrupted. Identification of the HIV reservoir and determining its mechanisms for persistence may aid in the development of strategies toward a cure for HIV. (This study was presented in part at the Conference on Retroviruses and Opportunistic Infections, Seattle, WA, February 23 to 26 2015.)
Synonymous Deoptimization of Foot-and-Mouth Disease Virus Causes Attenuation
In Vivo
while Inducing a Strong Neutralizing Antibody Response
Authors: Diaz-San Segundo Fayna , Medina Gisselle N. , Ramirez-Medina Elizabeth , Velazquez-Salinas Lauro , Koster Marla , Grubman Marvin J. , de los Santos Teresa
Published: November 2015

Codon bias deoptimization has been previously used to successfully attenuate human pathogens, including poliovirus, respiratory syncytial virus, and influenza virus. We have applied a similar technology to deoptimize the capsid-coding region (P1) of foot-and-mouth disease virus (FMDV). Despite the introduction of 489 nucleotide changes (19%), synonymous deoptimization of the P1 region rendered a viable FMDV progeny. The resulting strain was stable and reached cell culture titers similar to those obtained for wild-type (WT) virus, but at reduced specific infectivity. Studies in mice showed that 100% of animals inoculated with the FMDV A12 P1 deoptimized mutant (A12-P1 deopt) survived, even when the animals were infected at doses 100 times higher than the dose required to cause death by WT virus. All mice inoculated with the A12-P1 deopt mutant developed a strong antibody response and were protected against subsequent lethal challenge with WT virus at 21 days postinoculation. Remarkably, the vaccine safety margin was at least 1,000-fold higher for A12-P1 deopt than for WT virus. Similar patterns of attenuation were observed in swine, in which animals inoculated with A12-P1 deopt virus did not develop clinical disease until doses reached 1,000 to 10,000 times the dose required to cause severe disease in 2 days with WT A12. Consistently, high levels of antibody titers were induced, even at the lowest dose tested. These results highlight the potential use of synonymous codon pair deoptimization as a strategy to safely attenuate FMDV and further develop live attenuated vaccine candidates to control such a feared livestock disease.

IMPORTANCE
Foot-and-mouth disease (FMD) is one of the most feared viral diseases that can affect livestock. Although this disease appeared to be contained in developed nations by the end of the last century, recent outbreaks in Europe, Japan, Taiwan, South Korea, etc., have demonstrated that infection can spread rapidly, causing devastating economic and social consequences. The Global Foot-and-Mouth Disease Research Alliance (GFRA), an international organization launched in 2003, has set as part of their five main goals the development of next-generation control measures and strategies, including improved vaccines and biotherapeutics. Our work demonstrates that newly developed codon pair bias deoptimization technologies can be applied to FMD virus to obtain attenuated strains with potential for further development as novel live attenuated vaccine candidates that may rapidly control disease without reverting to virulence.