bluuebunny/crossref_metadata_2025 huggingface dataset:
New Methods for Qualification Assisted Innovation Applied to a Practical Example
Authors: McGeorge Dag , Åhjem Vidar , Borg Jonas
Published: August 2013

New technologies typically involve innovative aspects that are not addressed by existing normative standards and hence are not assessable through common certification procedures. To ensure that new technologies can be implemented in a safe and reliable manner, a specific kind of assessment is performed, which in many industries, e.g. the energy sector, is known as Technology Qualification (TQ). TQ aims at demonstrating with an acceptable level of confidence that a new technology will function within specified limits. DNV is currently developing a new method with application to Technology Qualification, drawing on the concept of assurance cases, based on a combination of function analysis originating from Value Engineering and argumentation logic used in safety cases. The method enables improved definition of the technology and where to focus when building confidence in it.

The method uses ‘Function Analysis’ that is structured towards what the system does instead of what it is. The focus on the functions encourages exploration of alternative ways by which the functions can be provided. Focus on functions draws attention to the system as a whole rather than each part the system consists of. This helps avoiding interface problems and may prove vital in an innovation process.

When the functions have been identified, one can proceed with analysing how a technical solution provides those functions. Those elements of the technical solution that represent proven technology can be dealt with by the conventional engineering processes and need not be included in the technology qualification process. Those elements assessed as new (or novel) are taken forward in the technology qualification process. This assessment is based both on the novelty of the function itself, the technical solution implementing it and the intended use of the technology in its intended environment. Confidence is demonstrated by first stating the goal of the qualification effort. Such a claim can be formulated as “The […] technology is fit for […]”. Then this goal is broken down into sub-goals. This is repeated till the lowest level claims can be directly justified by hard evidence. As an aid to overview and simplicity, such an argument structure (assurance case) can be presented graphically. The graphical assurance case can be readily communicated, reviewed and updated to reflect the needs and concerns of all stakeholders.

An on-going joint industry project for certification requirements to Deepwater Deployment and Recovery Systems will benefit from this improved method for qualification assisted innovation.
Inertia, Damping, and Wave Excitation of Heaving Coaxial Cylinders
Authors: Chau Fun Pang , Yeung Ronald W.
Published: August 2013

The method of matched eigenfunction expansions is applied in this paper to obtain the hydrodynamic coefficients of a pair of coaxial cylinders, each of which can have independent movement. The geometry idealizes a device for extracting ocean wave energy in the heave mode. The effects of geometric variations and the interaction between cylinders on the hydrodynamic properties are discussed. Analytical expressions for the low-frequency behavior of the hydrodynamic coefficients are also derived. The wave-exciting force on the bottom surface of either one of the cylinders is derived using the radiation solutions, with a generalized form of the Haskind relation developed for this geometry. The presented results are immediately applicable to examine free motion of coaxial cylinders in a wave field.
Prediction of Ship Response Statistics in Severe Sea Conditions Using RANS
Authors: Oberhagemann Jan , Ley Jens , el Moctar Bettar Ould
Published: August 2013

The International Association of Classification Societies (IACS) promotes the paradigm shift in structural design rules for ships towards risk based approaches. This requires improvements in the assessment of structural design loads and new methods for estimation of wave loads and responses, amongst others with respect to extreme value distributions. In this paper we present a numerical method based on the solution of RANS equations to deal with large wave-induced ship motions and corresponding loads for different ship types. Nonlinearities of wave excitation and ship response are included. Short-term ship response distributions from time domain simulations are compared with model test data. Significant deviations from Rayleigh distribution of amplitudes are observed, especially for hull girder loads including effects of structural elasticity.
Reliability Analysis of Mooring Lines for Deep Water Floating Systems
Authors: Gurumurthy K. , Ahmad Suhail , Chitrapu A. S.
Published: August 2013

Reliability analysis of mooring lines requires an accurate prediction of extreme responses for large number of sea states even for a short-term based approach. In deep water, the interactions between the floater motions and the large number of risers and mooring lines become significant and must be considered for accurate prediction of floater motions as well as line dynamics. Time-domain coupled dynamic analysis procedures have been shown to give more accurate results but at a higher computational expense. Therefore, efficient computational tools are required for reliability analysis of mooring lines for deep water floating systems. Enhanced decoupled dynamic analysis method, in which the floater motions are computed by coupled analysis considering a coarse finite element model of the mooring line, is an efficient method and provides results comparable in accuracy with the fully coupled dynamic analysis procedures. This paper presents the application of enhanced de-coupled dynamic analysis method for reliability assessment of mooring lines for deep water floating systems. For reliability analysis of mooring lines, the methodology presented in Ding et al. [5] is adopted. Reliability analysis of a critically loaded mooring line for a deep water classical spar floater under extreme environmental loads is performed using environmental contour approach. Mooring line tension time histories under various storm conditions are calculated using enhanced de-coupled dynamic analysis. The uncertainty in the predicted maximum mooring line load due to different storm events, variability in met-ocean conditions and numerical models is considered. Probability of failure and the corresponding reliability index of the mooring line are calculated. The impact of variability in predicted mooring line load, line capacities and factors of safety on mooring line reliability are studied. It is seen that enhanced de-coupled dynamic analysis, which predicts the mooring line loads as accurately as coupled dynamic analysis with lesser CPU time, can be used more efficiently for reliability assessment of mooring lines for deep water floating systems.
Study on Structural Form Design of Trimaran Cross-Deck
Authors: Ren Huilong , Zhen Chunbo , Li Chenfeng , Feng Guoqing
Published: August 2013

As a new high performance shipform, the structural form of trimaran is special and the stress concentration of its cross-deck structure is serious. According to the Rules for Classification of Trimaran Ships developed by Lloyd’s Register, the global finite element model of a trimaran is built. Main factors such as Thickness of bulkhead and wet deck, transitional forms and strengthening forms, which affect the stresses at local details are compared and discussed. Then the best structural form of trimaran cross-deck is given. The result can offer the reference for the trimaran’s design and development.
Experimental Study of Gas Production From Methane Hydrate by Depressurization and Combination Method Under Different Hydrate Saturations
Authors: Liu Liguo , Zhao Jiafei , Cheng Chuanxiao , Song Yongchen , Liu Weiguo , Liu Yu , Zhang Yi , Yang Zhi
Published: August 2013

In this work, different saturated methane hydrates were formed by controlling the methane gas filling pressure on the three-dimensional experimental systems. The hydrates were dissociated using by depressurization and combination method, respectively. The results indicated that, as the saturation enhancing, the gas production was enlarged, however, the gas production rate became extremely volatile, and the decomposition cycle increased. Furthermore, compared with single depressurization, the combination method has the high gas production rate and efficiency, and the short decomposition cycle. So the combination method is worthy for further study of the gas hydrate exploitation.
From Design to Installation of the 2nd Generation of Integrated Production Bundle Riser (IPB)
Authors: Decoret Laurent , Lecroq Gerald
Published: August 2013

As part of the TOTAL E&P Angola (TEPA) PAZFLOR development, two 10” Integrated Production Bundle (IPB) flexible risers have been installed to connect the Pipe-In-Pipe Oligocene loop to the FPSO.

While IPB risers have first been implemented on the nearby DALIA development, the PAZFLOR IPB had to accommodate much higher design and operating temperatures. From the on-set of the project, focus was put on improving the design of this second generation of IPB and ensuring that all the lessons learnt from DALIA were addressed from a design, manufacturing and installation point of view. The paper presents the main elements of the IPB design as well as the comprehensive set of specific qualification tests performed during the course of the project. Indeed new materials were qualified, a new end fitting design for the bundle was implemented and various mechanical and thermal full scale tests were performed.

Both risers have now been successfully installed and commissioned further proving that IPB flexible risers are a technical and cost effective solution to address the flow assurance challenges of deep water production fluid recovery.
Integrating Constrained Random Waves in Endurance Time Analysis of Offshore Structures Subjected to Sea Waves
Authors: Nikoo H. Matin , Zeinoddini M. , Estekanchi H. , Golestani M.
Published: August 2013

This paper introduces a novel methodology for design and assessment of offshore structures exposed to irregular sea waves. For this, Constrained NewWave (CNW) is integrated with the Endurance Time Analysis (ETA) methodology, which is basically developed for the performance based analysis of onshore structures to earthquake loads. In this approach, the offshore structure is simulated in time-domain under a set of calibrated intensifying wave functions. They are devised to represent a gradually increasing roughness of the sea state by time. A performance index such as base shear, drift or stress in a critical structural members are monitored until they reach to a predefined maximum value. A higher endurance time (corresponding to a higher wave height) is to be interpreted as a better performance of structure.

Ability to consider spectral features of waves, waves’ irregularity, the wave-in-deck impacts, utilizing a relatively simple approach, requiring relatively low computational times and capability to consider any desirable damage indices are the advantages of this novel method. The method can be used in the design stage, collapse analysis and for the assessment of existing offshore platforms.

In this paper the effectiveness of this method has been examined on offshore jacket platforms. The results obviously have highlighted the potentials of this approach for the dynamic, time-domain, non-linear analysis and assessment of offshore platforms.
A Framework for Hurricane Risk Assessment of Offshore Wind Farms
Authors: Kim E. , Manuel L.
Published: August 2013

We present a framework aimed at estimating the potential damage to an offshore wind farm from hurricanes. Our approach is related to assessing risks that are assumed to be fundamentally related to the estimation of wind speed exceedance probabilities at selected hub heights of wind turbines in the farm and of associated wind turbine loads. As part of this preliminary framework for risk assessment, synthetic storm tracks are first simulated over the ocean using available historical tropical storm data; then, a hurricane intensity evolution model based on thermodynamic and atmospheric environmental variables is developed for each of the tracks as they get to regions within the proximity of the chosen wind farm site. Based on this intensity model, a turbulent wind field can be simulated at locations of interest along the hurricane track. The simulated turbulent wind field may then be used to estimate wind speed exceedance probability distributions and, when combined with correlated waves, it can also be used in analysis of the response of individual turbines in a wind farm. The framework for the overall risk assessment is presented; the individual components that comprise such an assessment are described briefly in illustrative applications.
Effect of the Sodium and Potassium Chloride on the Mechanical and Plastic Properties on the Oil Well Cement Slurries
Authors: Abelha Rocha Camila Aparecida , Simão Cristina Aiex , Cordeiro Guilherme Chagas , Toledo Filho Romildo Dias
Published: August 2013

In recent times, a large reserve of oil and gas in a Pre-Salt zone has been identified in Brazil. In this reserve it is necessary to drill and cement a layer of approximately 2.000 meters of salt rock. In salt rocks, the contact of cement with the rock during the cementing operation can cause the dissolution of the rock and salt can migrate to the cement slurry. Cementitious systems containing salt in their composition have been proposed to minimize the transport of rock salt to the slurry. Considering that the presence of salt can cause changes in the properties of the slurry and compromises the cementing quality. Studies are necessary to understand how the type and concentration of salt can affect the short and long term behavior of the slurry. In this work, the effect of the amount of sodium chloride (NaCl) and potassium chloride (KCl) on the properties of the oil well cement slurry was studied. For this, slurries containing 5%, 10%, 12.5%, 15%, 17.5%, 20% and 36% NaCl by the weight of water (BWOW), and 1%, 3%, 5%, 7%, 10% and 34% KCl (BWOW) were designed. The effect of salt type and content on the rheology, free-fluid and mechanical properties such as compression strength, Young’s modulus, Poisson’s rate and splitting tension strength was investigated. The mechanical properties were evaluated at an age of 8 hours of curing in water at 38°C (100° F) and 60° C (140° F) and 7 days of curing in water at 60° C. The addition of NaCl and KCl resulted in similar behavior in almost all the properties studied. The properties of freshly and early-age, as free-fluid and compression strength, of saline slurry differed in two different mechanisms depending by the salt concentration. For other side, in most cases, the rheological and long-age properties were reduced with an increase in salt content.
Study of Kinetic, Structure and Properties Evaluation of Organically Modified Montmorillonites and Micro Nanocellulose Added to Cement Paste
Authors: Vazquez Analía , Piqué Teresa M. , Hoyos Catalina Gómez , Escobar Mariano M.
Published: August 2013

The effect of the addition of cellulose microfibrils, water soluble polymer, nanoclays and carbon nanotubes to the cement paste was studied. The hydration kinetic was determined by means of an adiabatic rise temperature method. The addition of polymer to the cement paste produced the highest delay in the hydration kinetic followed by the addition of organically modified montmorillonites in a polymer solution. Flexion and compression strength were determined. Some admixtures produced an increase of the cement paste’s void content. Cellulose produced a change in the rheology and a delay in the hydration kinetic of the cement paste. The use of heat for curing increased the mortar’s mechanical properties. Carbon nanotubes also were added to the cement paste in order to study the effect on electric conductivity and hydration kinetic.
A New Safety and Stability Enhanced Riser Control System: An Integrated Hybrid Riser Tensioning System
Authors: Wu Yin , Bourgeau Edward P. K. , Baldick Ross
Published: August 2013

This paper presents the framework for a novel riser tensioning system using a hybrid arrangement for energy management. This hybrid tensioning system, which integrates electrical tensioners and energy storage elements with existing hydro-pneumatic tensioners, is designed to enhance the safety of a deepwater riser system by improving stability and dynamic performance. Four control modes are investigated for the framework implementation: 1. Normal operation mode for active heave compensation. 2. Riser-recoil mode to control recoil on sudden release and minimize unwanted riser upward movement. 3. VIV suppression mode to reduce disturbances induced by ocean currents in the riser string and to extend riser fatigue life. 4. Reconnection mode provides control to allow reconnecting the LMRP to the BOP without using the drawworks, freeing the drawworks from the time consuming procedure of landing the LMRP and tensioning the riser. A replacement strategy is proposed so that one can update any existing system to the hybrid riser tensioning system by replacing certain pairs of hydro-pneumatic tensioners with the novel electrical riser tensioners to achieve smooth system upgrade and better system reliability.
A Numerical Investigation Into the Bottom Boundary Effect for Spudcan Penetration on Sand Overlying Clay in Centrifuge Test
Authors: Ullah Shah Neyamat , Hu Yuxia
Published: August 2013

In the last two decades centrifuge testing of geomaterials to meet offshore design has gained momentum. In the absence of large scale testing this technique with all its versatility has been successfully used for many offshore applications encompassing spudcan foundation, anchors, caissons, piles etc. Although many real soil failure characteristics can be replicated in the centrifuge, the centrifuge strong box may constrain the testing range when large displacement of spudcan foundation needs to be tested, especially in multiple layer soils. The paper investigates the rigid bottom boundary effect of the centrifuge strong box during large penetration of spudcan foundation into sand over clay soil profiles. Large deformation finite element (LDFE) method incorporating RITSS (Remeshing and Interpolation Technique using Small Strain) approach has been adopted for numerical simulation of the problem. With fixed vertical space available, the effects of sand layer thickness, sand friction and dilation angles have been studied. The LDFE/RITSS method was validated by existing centrifuge test data. It was observed that, during spudcan penetration, the development of sand plug trapped beneath the spudcan played a crucial role in the bottom boundary effect. The boundary effect started earlier when the ratio of sand layer thickness to spudcan diameter was greater than unity.
Wave Energy Hyperbaric Converter: Small Scale Models, Prototype and Control Strategies
Authors: Estefen Segen F. , Garcia-Rosa Paula B. , Ricarte Eliab , da Costa Paulo Roberto , Pinheiro Marcelo M. , Lourenço Marcelo I. , Machado Isaac R. , Maes Sergio R.
Published: August 2013

A device for electricity generation from ocean waves has been developed for installation on the Brazilian northeast coast. It is based on pumping modules and a two-stage accumulator linked to a hyperbaric chamber in order to provide a prescribed high pressure water flow, which operates a turbine coupled with an electrical generator. In the period between 2001 and 2007, wave tank testing of small-scale models have been carried out. A prototype with two pumping modules is presently installed in the Port of Pecém. This paper describes an overview of the device development since the first tests to the installation of the prototype. Wave climate analysis, design analysis and optimization studies have been developed and are briefly revised in this study. Furthermore, control strategies are proposed to optimize the electrical output considering the proper combination of both pressure and flow rate as a function of the predominant wave climate, when the applied pressure is constant and the generator is a synchronous machine.
Motion Response Control of the DWSC Spar Based on State-Space Model
Authors: Yu Xiaochuan , Falzarano Jeffrey
Published: August 2013

In 2007, the Office of Naval Research (ONR) started a technology development program called STLVAST (Small to Large Vessel At-Sea Transfer), in order to develop ‘enabling capabilities’ in the realm of logistic transfer (i.e. stores, equipment, vehicles) between a large transport vessel and a smaller T-craft ship, using a Deep Water Stable Crane (DWSC) spar between them.

In this paper, the equation of motions of the single DWSC spar is initially expressed as the standard state-space model. Then the ODE solver of Matlab is directly employed to obtain the motion responses at each time step. Two levels of approximation of hydrodynamic coefficients are considered in this study. One is the Constant Coefficient Method (CCM), and the other one is the Impulse Response Function (IRF) method, with fluid memory effects considered. WAMIT software is used to calculate the hydrodynamic coefficients, including the added mass, radiation damping, IRF, the first order and second order waves loads transfer functions, etc. The motion response control is achieved by assuming the thrusters can provide the optimal feedback force derived from Linear Quadratic Regulator (LQR) method.
Megacity Megaquakes—Two Near Misses
Authors: Stein Ross S. , Toda Shinji
Published: August 2013

Seismicity patterns after large earthquakes suggest that the earthquake hazard can rise sharply in areas well beyond the mainshock rupture zone.
Conformational Motions Regulate Phosphoryl Transfer in Related Protein Tyrosine Phosphatases
Authors: Whittier Sean K. , Hengge Alvan C. , Loria J. Patrick
Published: August 2013

Closing the Loop

Many studies have shown that protein dynamics are important to enzyme function. For example, enzyme protein movements have been shown to optimize the active site, enable binding of substrate and cofactor, and facilitate product release.

Whittier
et al.

(p.
899
) now show that in two tyrosine phosphatases, the rate of cleavage is coupled to motion of a loop. The two phosphatases have different catalytic rates; however, in both, a loop containing a catalytic residue switches between an inactive open and a catalytically competent closed state. The rates of closure are equivalent to the cleavage rates, suggesting that the leaving group tyrosine is protonated simultaneously with loop closure. Thus, tuning of the loop motion plays a regulatory role in the catalytic cycle.
Gene Therapy That Works
Authors: Verma Inder M.
Published: August 2013

Gene therapy trials show a beneficial effect in children suffering from a neurodegenerative disorder or an immunodeficiency disease.

[Also see Research Articles by

Biffi
et al.

and

Aiuti
et al.

]
Nucleation from Solution
Authors: Myerson Allan S. , Trout Bernhardt L.
Published: August 2013

Computer simulations of crystal nucleation provide evidence for two-step nucleation.

[Also see Report by

Wallace
et al.

]
Half of All Papers Now Free in Some Form, Study Claims
Authors: Kaiser Jocelyn
Published: August 2013

One-half of all scientific papers published each year are now available in some kind of free, "open-access" format, a new study claims, marking a tipping point in technical publishing.
The CRISPR Craze
Authors: Pennisi Elizabeth
Published: August 2013

A bacterial immune system yields a potentially revolutionary genome-editing technique.
The Save-the-World Foundation
Authors: Irion Robert
Published: August 2013

Convinced that NASA will not finish the job, a private foundation intends to raise $450 million for a space mission to find asteroids that may threaten Earth.
Genome Sequence of Salmonella enterica Serovar Typhi Oral Vaccine Strain Ty21a
Authors: Xu DeQi , Cisar John O. , Poly Frédéric , Yang Jinghua , Albanese Jason , Dharmasena Madushini , Wai Tint , Guerry Patricia , Kopecko Dennis J.
Published: August 2013

Attenuated
Salmonella enterica
serovar Typhi strain Ty21a is an important vaccine for controlling typhoid fever and serves as an oral vector for delivering heterologous antigens. The key attenuating features of this randomly mutated strain remain in question. Genome sequencing has revealed 679 single nucleotide polymorphisms (SNPs), and will help define alterations contributing to Ty21a safety and immunogenicity.
Complete Genomic Sequences of an H3N8 Equine Influenza Virus Strain Isolated in China
Authors: Zhu Chao , Li Qian , Guo Wei , Lu Gang , Yin Xin , Qi Ting , Xiang Wenhua , Ran Duoliang , Qu Juanjuan
Published: August 2013

We report the complete genomic sequence of A/equine/Heilongjiang/1/2010, a strain of Florida sublineage clade 2 of H3N8 subtype equine influenza virus (EIV) isolated in northern China. This is the first announcement of a complete genomic sequence of EIV of such a clade in China.
Draft Genome Sequence of Lactobacillus pasteurii CRBIP 24.76
T
Authors: Cousin Sylvie , Clermont Dominique , Creno Sophie , Ma Laurence , Loux Valentin , Bizet Chantal , Bouchier Christiane
Published: August 2013

We report the draft genome sequence of the type strain
Lactobacillus pasteurii
CRBIP 24.76, which is closely related to
L. gigeriorum
CRBIP 24.85
T
, isolated from a chicken crop. The total length of the 29 contigs is about 1.9 Mb, with a G+C content of 40% and 1,946 coding sequences.
Draft Genome Sequence of Holospora undulata Strain HU1, a Micronucleus-Specific Symbiont of the Ciliate
Paramecium caudatum
Authors: Dohra Hideo , Suzuki Haruo , Suzuki Tomohiro , Tanaka Kenya , Fujishima Masahiro
Published: August 2013

Holospora undulata
is a micronucleus-specific symbiont of the ciliate
Paramecium caudatum
. We report here the draft genome sequence of
H. undulata
strain HU1. This genome information will contribute to the study of symbiosis between
H. undulata
and the host
P. caudatum
.
Identification, Typing, and Phylogenetic Relationships of the Main Clinical Nocardia Species in Spain According to Their
gyrB
and
rpoB
Genes
Authors: Carrasco Gema , Valdezate Sylvia , Garrido Noelia , Villalón Pilar , Medina-Pascual Maria J. , Sáez-Nieto Juan A.
Published: August 2013

This study compares the identification, typing, and phylogenetic relationships of the most prevalent clinical
Nocardia
species in Spain, as determined via sequence analysis of their housekeeping genes
gyrB
and
rpoB
, with the results returned by the gold standard 16S rRNA method.
gyrB
and
rpoB
analyses identified
Nocardia abscessus
,
N. cyriacigeorgica
,
N. farcinica
, and the
N. nova
complex, species that together account for more than half of the human nocardiosis cases recorded in Spain. The individual discriminatory power of
gyrB
and
rpoB
with respect to intraspecies typing, calculated using the Hunter-Gaston discriminatory index (HGDI), was generally high (HGDI, 0.85 to 1), except for
rpoB
with respect to
N. farcinica
(HGDI, 0.71). Phylogenetically, different degrees of intra- and interspecies microheterogeneity were observed for
gyrB
and
rpoB
in a group of 119 clinical strains. A single 16S haplotype was obtained for each species, except for the
N. nova
complex (8 types), while
gyrB
and
rpoB
were more polymorphic:
N. abscessus
had 14 and 18 haplotypes,
N. cyriacigeorgica
had 17 and 12,
N. farcinica
had 11 and 5, and the
N. nova
complex had 26 and 29 haplotypes, respectively. A diversity gradient was therefore seen, with
N. farcinica
at the bottom followed by
N. abscessus
and
N. cyriacigeorgica
in the middle and
N. nova
complex at the top. The complexity of the
N. nova
complex is highlighted by its six variations in the GyrB
126
AAAPEH motif.
gyrB
sequencing (with or without
rpoB
sequencing) offers a simple means for identifying the most prevalent
Nocardia
species in Spanish medical laboratories and for determining the intraspecific diversity among their strains.
Anal Human Papillomavirus Genotype Distribution in HIV-Infected Men Who Have Sex with Men by Geographical Origin, Age, and Cytological Status in a Spanish Cohort
Authors: Torres Montserrat , González Cristina , del Romero Jorge , Viciana Pompeyo , Ocampo Antonio , Rodríguez-Fortúnez Patricia , Masiá Mar , Blanco José Ramón , Portilla Joaquín , Rodríguez Carmen , Hernández-Novoa Beatriz , del Amo Julia , Ortiz Marta
Published: August 2013

Knowledge of human papillomavirus (HPV) type distribution in populations at risk for anal cancer is needed. Here, we describe the anal HPV genotype distribution in a large Spanish cohort (Cohort of the Spanish HIV Research Network HPV [CoRIS-HPV]) of HIV-positive men who have sex with men (MSM) according to geographical origin, age, and cytological status. A cross-sectional analysis of baseline data from 1,439 HIV-infected MSM (2007 to 2012) was performed. Anal HPV genotyping was performed using the Linear Array HPV genotyping test. Descriptive analyses of subject characteristics, prevalences, and 95% confidence intervals (CI) were performed. The global prevalences of HPV, high-risk HPV (HR-HPV), and low-risk HPV (LR-HPV) types were 95.8%, 83.0%, and 72.7%, respectively. Among the HR-HPV types, HPV16 was the most common, followed by HPV59, -39, -51, -18, and -52. The prevalence of multiple HR-HPV infections was 58.5%. There were no differences in the crude analyses between Spanish and Latin-American MSM for most HPV types, and a peak in prevalence for most HPV types was seen in patients in their late thirties. Globally and by specific HPV groups, men with abnormal anal cytologies had a higher prevalence of infection than those with normal cytologies. This study has the largest number of HIV-positive MSM with HPV genotype data analyzed according to cytological status as far as we know. The information gained from this study can help with the design of anal cancer prevention strategies in HIV-positive patients.
Correlation between Clostridium difficile Bacterial Load, Commercial Real-Time PCR Cycle Thresholds, and Results of Diagnostic Tests Based on Enzyme Immunoassay and Cell Culture Cytotoxicity Assay
Authors: Dionne Léa-Laurence , Raymond Frédéric , Corbeil Jacques , Longtin Jean , Gervais Philippe , Longtin Yves
Published: August 2013

The impact of
Clostridium difficile
fecal loads on diagnostic test results is poorly understood, but it may have clinical importance. In this study, we investigated the relationship between
C. difficile
fecal load and the results of four assays: a glutamate dehydrogenase (GDH) enzyme immunoassay (EIA), a toxin A/B antigen EIA (ToxAB), a cell culture cytotoxicity assay (CCA), and PCR targeting the
tcdB
gene. We also compared the PCR cycle threshold (

C
T

) with the results of quantitative culture using Spearman's rank correlation coefficient. Finally, we sequenced the genomes of 24 strains with different detection profiles. A total of 203 clinical samples harboring toxigenic
C. difficile
were analyzed and sorted into one of four groups: 17 PCR
+
(group 1), 37 PCR
+
GDH
+
(group 2), 24 PCR
+
GDH
+
CCA
+
(group 3), and 125 PCR
+
GDH
+
ToxAB
+
(group 4). The overall median fecal load in log
10
CFU/g was 6.67 (interquartile range [IQR], 5.57 to 7.54). The median fecal bacterial load of groups 1, 2, 3, and 4 were 4.15 (IQR, 3.00 to 4.98), 5.74 (IQR, 4.75 to 6.16), 6.20 (IQR, 5.23 to 6.80), and 7.08 (IQR, 6.35 to 7.83), respectively. Group 1 samples had lower fecal loads than those from each of the other groups (
P
< 0.001). Group 2 samples had lower fecal loads than those from groups 3 and 4 (
P
< 0.001). There was a significant correlation between PCR

C
T

and fecal loads (ρ = −0.697;
P
< 0.001). NAP1 strains were associated with the detection of toxins by EIA or CCA (
P
= 0.041). This study demonstrates an association between
C. difficile
fecal load and the results of routinely used diagnostic tests.
Serotype 5 Pneumococci Causing Invasive Pneumococcal Disease Outbreaks in Barcelona, Spain (1997 to 2011)
Authors: Rolo Dora , Fenoll Asunción , Fontanals Dionísia , Larrosa Nieves , Giménez Montserrat , Grau Immaculada , Pallarés Román , Liñares Josefina , Ardanuy Carmen ,   the Serotype 5 Study Group
Published: August 2013

In this study, we analyzed the clinical and molecular epidemiology of invasive serotype 5 (Ser5) pneumococcal isolates in four teaching hospitals in the Barcelona, Spain, area (from 1997 to 2011). Among 5,093 invasive pneumococcal isolates collected, 134 (2.6%) Ser5 isolates were detected. Although the overall incidence of Ser5-related invasive pneumococcal disease (IPD) was low (0.25 cases/100,000 inhabitants), three incidence peaks were detected: 0.63/100,000 in 1999, 1.15/100,000 in 2005, and 0.37/100,000 in 2009. The rates of Ser5 IPD were higher among young adults (18 to 64 years old) and older adults (>64 years old) in the first two peaks, whereas they were higher among children in 2009. The majority (88.8%) of the patients presented with pneumonia. Comorbid conditions were present in young adults (47.6%) and older adults (78.7%), the most common comorbid conditions being chronic obstructive pulmonary disease (20.6% and 38.3%, respectively) and cardiovascular diseases (11.1% and 38.3%, respectively). The mortality rates were higher among older adults (8.5%). All Ser5 pneumococci tested were fully susceptible to penicillin, cefotaxime, erythromycin, and ciprofloxacin. The resistance rates were 48.5% for co-trimoxazole, 6.7% for chloramphenicol, and 6% for tetracycline. Two major related sequence types (STs), ST1223 (
n
= 65) and ST289 (
n
= 61), were detected. The Colombia
5
-ST289 clone was responsible for all the cases in the Ser5 outbreak in 1999, whereas the ST1223 clone accounted for 73.8% and 61.5% of the isolates in 2005 and 2009, respectively. Ser5 pneumococci are a frequent cause of IPD outbreaks in the community and involve children and adults with or without comorbidities. The implementation of the new pneumococcal conjugated vaccines (PCV10 and PCV13) might prevent such outbreaks.
Novel Approach for Improving Sensitivity of Microscopic Detection of Acid-Fast Bacilli (AFB) by Use of the ReaSLR Method
Authors: Verma Sheetal , Dhole Tapan N. , Kumar Manoj , Kashyap Saurabh
Published: August 2013

The ReaSLR methodology developed for sputum processing is a novel, low-cost, and simple technique that has improved the sensitivity of smear microscopy for the diagnosis of tuberculosis (TB). Sample processing consists of rapid liquefaction of the sputum specimen with the ReaSLR reagent, followed by syringe filtration, concentration by centrifugation, and use of the sediment for smear microscopy. The performance of the ReaSLR kit was evaluated on 150 sputum samples and was compared with that of the modified Petroff method for sputum decontamination and concentration. Ziehl-Neelsen staining was performed for smear microscopy after processing by these two techniques; simultaneously, culture on Lowenstein-Jensen (LJ) medium was done to evaluate the two methods. The efficiency of smear microscopy was 18/150 (12%) with the modified Petroff method compared to 47/150 (31.33%) with the ReaSLR method, and this difference was statistically significant (
P
< 0.001). The ReaSLR method for smear microscopy demonstrated a sensitivity and specificity of 90.47% and 91.6%, respectively, whereas the modified Petroff method showed a sensitivity and specificity of 40.47% and 99.07%, respectively, compared to those of culture, which was used as the gold standard. With the newer ReaSLR method, the kappa coefficient (κ) was 0.8, which implies an excellent positive agreement. The ReaSLR method was found to be more sensitive than the conventional method for sputum smear microscopy. The newer ReaSLR method holds promise for adoption in TB control programs across the globe, as it was found suitable for the laboratory diagnosis of pulmonary TB. Further large-scale studies are needed to evaluate other aspects of this method.
Comparison of Matrix-Assisted Laser Desorption Ionization–Time of Flight (MALDI-TOF) Mass Spectrometry Platforms for the Identification of Gram-Negative Rods from Patients with Cystic Fibrosis
Authors: Alby Kevin , Gilligan Peter H. , Miller Melissa B.
Published: August 2013

We evaluated the performance of the Bruker Biotyper and the bioMérieux Vitek MS with both the SARAMIS v4.09 and Knowledge Base v2.0 databases for the identification of 203 non-glucose-fermenting Gram-negative rods that had previously been identified by 16S rRNA gene sequencing. Including those that underwent repeat testing, 96.6%, 90.1%, and 93.6% of isolates, respectively, had identifications that agreed with the previous identification.
Validation of an
rpoB
Gene PCR Assay for Detection of Tropheryma whipplei: 10 Years' Experience in a National Reference Laboratory
Authors: Moter Annette , Schmiedel Dinah , Petrich Annett , Wiessner Alexandra , Kikhney Judith , Schneider Thomas , Moos Verena , Göbel Ulf B. , Reischl Udo
Published: August 2013

The performance of a real-time PCR assay targeting the
Tropheryma whipplei
rpoB
gene was evaluated using test strains and 1,236 clinical specimens in a national reference laboratory. The novel
rpoB
-PCR assay proved to be specific, revealed improved analytical sensitivity, and substantially accelerated detection of
T. whipplei
DNA in clinical specimens.
Rapid and Direct Real-Time Detection of
bla
KPC
and
bla
NDM
from Surveillance Samples
Authors: Vasoo Shawn , Cunningham Scott A. , Kohner Peggy C. , Mandrekar Jayawant N. , Lolans Karen , Hayden Mary K. , Patel Robin
Published: August 2013

We assessed the performance of a duplex real-time PCR assay for
bla
KPC
and
bla
NDM
performed directly (D-PCR) on perianal and perirectal swabs and stool. Spiked specimens and 126 clinical surveillance swabs (comprising a sensitivity panel of 46 perirectal double swabs previously determined to be culture positive for
bla
KPC
-PCR-positive
Enterobacteriaceae
and a specificity panel of 80 perianal swabs from patients at risk of carbapenemase-producing
Enterobacteriaceae
[CPE] colonization) were studied. For the surveillance swabs, D-PCR was compared to PCR after broth enrichment (BE-PCR) and two culture-based methods: the HardyCHROM ESBL agar (HC-A) and the CDC screening (CDC-A) methods. PCR was performed on morphologically distinct colonies that were isolated by culture. All of the initial PCR testing was done without extraction using a simple lysis procedure. The analytical sensitivities of D-PCR for
bla
KPC
were 9 CFU/μl (for swabs) and 90 CFU/μl (for stool), and for
bla
NDM
, it was 1.9 CFU/μl (for both swabs and stool). In the clinical sensitivity panel, D-PCR and BE-PCR were initially positive for
bla
KPC
in 41/46 (89.1%) and 43/46 (93.5%) swabs, respectively. The swabs that were initially negative by D-PCR (
n
= 5) and BE-PCR (
n
= 3) were visibly stool soiled; all swabs were
bla
KPC
positive upon repeat testing after lysate extraction. The CDC-A and HC-A yielded
bla
KPC
-positive
Enterobacteriaceae
from 36/46 (78.3%) and 35/46 (76.1%) swabs, respectively (sensitivities of D-PCR/BE-PCR postextraction of soiled specimens versus HC-A,
P
= 0.0009, and versus CDC-A,
P
= 0.0016). All swabs in the specificity panel were negative for CPE by all four methods. D-PCR allows for the timely detection of
bla
KPC
and
bla
NDM
carriage with excellent sensitivity when specimens visibly soiled with stool undergo preparatory extraction.
Evaluation of an Enzyme Immunoassay for Detection of Histoplasma capsulatum Antigen from Urine Specimens
Authors: Theel Elitza S. , Jespersen Deborah J. , Harring Julie , Mandrekar Jay , Binnicker Matthew J.
Published: August 2013

Detection of
Histoplasma capsulatum
urinary antigen (UAg) is important for the initial diagnosis of infection and for monitoring of patient responses to antifungal therapy. This study evaluated an analyte-specific reagent (ASR) enzyme immunoassay (EIA) for the detection of
H. capsulatum
UAg from Immuno Mycologics, Inc. (IMMY) (Norman, OK) in comparison with routine testing with the MiraVista (MVista)
H. capsulatum
quantitative EIA (MiraVista Diagnostics, Indianapolis, IN). Using prospectively collected urine specimens (
n
= 1,003), we observed an overall percent agreement between the two assays of 97.6% (979/1,003 samples). Compared with the MVista EIA, the sensitivity and specificity of the IMMY ASR EIA were 64.5% (40/62 samples) and 99.8% (939/941 samples), respectively, using a cutoff value of 0.5 ng/ml. Based on available clinical histories for 23/24 discordant samples, 5 IMMY assay-negative/MVista assay-positive samples were considered falsely positive. Furthermore, 10/23 discordant samples were positive by the MVista EIA but were below the limit of quantitation (<0.4 ng/ml). The clinical significance of these low positive results in the MVista EIA is unclear. In addition to the prospective study, we tested 11 urine specimens collected from patients with culture-confirmed
Histoplasma
infections, and 100% (11/11 samples) were positive by the IMMY ASR EIA. In conclusion, the IMMY ASR EIA may offer an alternative approach for the detection of
Histoplasma
UAg. Additional prospective studies are needed to better characterize the performance of the IMMY ASR EIA in conjunction with clinical and laboratory findings.
Inhibition of Megakaryocyte Development in the Bone Marrow Underlies Dengue Virus-Induced Thrombocytopenia in Humanized Mice
Authors: Sridharan Aishwarya , Chen Qingfeng , Tang Kin Fai , Ooi Eng Eong , Hibberd Martin L. , Chen Jianzhu
Published: August 2013

A characteristic clinical feature of dengue virus infection is thrombocytopenia, though its underlying mechanism is not definitively determined. By adoptive transfer of human CD34+fetal liver cells into immunodeficient mice, we have constructed humanized mice with significant levels of human platelets, monocytes/macrophages, and hepatocytes. Infection of these mice with both lab-adapted and clinical strains of dengue virus induces characteristic human hematological changes, including transient leukopenia and thrombocytopenia. We show that the specific depletion of human platelets is not mediated by antibodies in the periphery or reduced production of human thrombopoietin in the liver but reduction of human megakaryocytes and megakaryocyte progenitors in the bone marrow of the infected mice. These findings identify inhibition of platelet production in the bone marrow as a key mechanism underlying dengue-induced thrombocytopenia and suggest the utility of the improved humanized mouse model in studying dengue virus infection and pathogenesis in a human cell context.
Phosphorylation of Measles Virus Nucleoprotein Affects Viral Growth by Changing Gene Expression and Genomic RNA Stability
Authors: Sugai Akihiro , Sato Hiroki , Yoneda Misako , Kai Chieko
Published: August 2013

The measles virus (MV) nucleoprotein associates with the viral RNA genome to form the N-RNA complex, providing a template for viral RNA synthesis. In our previous study, major phosphorylation sites of the nucleoprotein were identified as S479 and S510. However, the functions of these phosphorylation sites have not been clarified. In this study, we rescued recombinant MVs (rMVs) whose phosphorylation sites in the nucleoprotein were substituted (rMV-S479A, rMV-S510A, and rMV-S479A/S510A) by reverse genetics and used them in subsequent analyses. In a one-step growth experiment, rMVs showed rapid growth kinetics compared with wild-type MV, although the peak titer of the wild-type MV was the same as or slightly higher than those of the rMVs. Time course analysis of nucleoprotein accumulation also revealed that viral gene expression of rMV was enhanced during the early phase of infection. These findings suggest that nucleoprotein phosphorylation has an important role in controlling viral growth rate through the regulation of viral gene expression. Conversely, multistep growth curves revealed that nucleoprotein-phosphorylation intensity inversely correlated with viral titer at the plateau phase. Additionally, the phosphorylation intensity of the wild-type nucleoprotein in infected cells was significantly reduced through nucleoprotein-phosphoprotein binding. Excessive nucleoprotein-phosphorylation resulted in lower stability against RNase and faster turnover of viral genomic RNA. These results suggest that nucleoprotein-phosphorylation is also involved in viral genomic RNA stability.
Pattern Recognition Receptor MDA5 Modulates CD8
+
T Cell-Dependent Clearance of West Nile Virus from the Central Nervous System
Authors: Lazear Helen M. , Pinto Amelia K. , Ramos Hilario J. , Vick Sarah C. , Shrestha Bimmi , Suthar Mehul S. , Gale Michael , Diamond Michael S.
Published: August 2013

Many viruses induce type I interferon responses by activating cytoplasmic RNA sensors, including the RIG-I-like receptors (RLRs). Although two members of the RLR family, RIG-I and MDA5, have been implicated in host control of virus infection, the relative role of each RLR in restricting pathogenesis
in vivo
remains unclear. Recent studies have demonstrated that MAVS, the adaptor central to RLR signaling, is required to trigger innate immune defenses and program adaptive immune responses, which together restrict West Nile virus (WNV) infection
in vivo
. In this study, we examined the specific contribution of MDA5 in controlling WNV in animals.
MDA5
−/−
mice exhibited enhanced susceptibility, as characterized by reduced survival and elevated viral burden in the central nervous system (CNS) at late times after infection, even though small effects on systemic type I interferon response or viral replication were observed in peripheral tissues. Intracranial inoculation studies and infection experiments with primary neurons
ex vivo
revealed that an absence of MDA5 did not impact viral infection in neurons directly. Rather, subtle defects were observed in CNS-specific CD8
+
T cells in
MDA5
−/−
mice. Adoptive transfer into recipient
MDA5
+/+
mice established that a non-cell-autonomous deficiency of MDA5 was associated with functional defects in CD8
+
T cells, which resulted in a failure to clear WNV efficiently from CNS tissues. Our studies suggest that MDA5 in the immune priming environment shapes optimal CD8
+
T cell activation and subsequent clearance of WNV from the CNS.
Nuclear Relocalization of Polyadenylate Binding Protein during Rift Valley Fever Virus Infection Involves Expression of the NSs Gene
Authors: Copeland Anna Maria , Altamura Louis A. , Van Deusen Nicole M. , Schmaljohn Connie S.
Published: August 2013

Rift Valley fever virus (RVFV), an ambisense member of the family
Bunyaviridae
, genus
Phlebovirus
, is the causative agent of Rift Valley fever, an important zoonotic infection in Africa and the Middle East. Phlebovirus proteins are translated from virally transcribed mRNAs that, like host mRNA, are capped but, unlike host mRNAs, are not polyadenylated. Here, we investigated the role of PABP1 during RVFV infection of HeLa cells. Immunofluorescence studies of infected cells demonstrated a gross relocalization of PABP1 to the nucleus late in infection. Immunofluorescence microscopy studies of nuclear proteins revealed costaining between PABP1 and markers of nuclear speckles. PABP1 relocalization was sharply decreased in cells infected with a strain of RVFV lacking the gene encoding the RVFV nonstructural protein S (NSs). To determine whether PABP1 was required for RVFV infection, we measured the production of nucleocapsid protein (N) in cells transfected with small interfering RNAs (siRNAs) targeting PABP1. We found that the overall percentage of RVFV N-positive cells was not changed by siRNA treatment, indicating that PABP1 was not required for RVFV infection. However, when we analyzed populations of cells producing high versus low levels of PABP1, we found that the percentage of RVFV N-positive cells was decreased in cell populations producing physiologic levels of PABP1 and increased in cells with reduced levels of PABP1. Together, these results suggest that production of the NSs protein during RVFV infection leads to sequestration of PABP1 in the nuclear speckles, creating a state within the cell that favors viral protein production.