bluuebunny/crossref_metadata_2025 huggingface dataset:
Diversity in weed seed production and the soil seed bank: Contrasting responses between two agroecosystems
Authors: Srivastava Rajani , Singh K.P.
Published: December 2013

This study was carried out to compare the diversity in seed production and the soil seed bank in a dryland and an irrigated agroecosystem in the dry tropics. Both agroecosystems showed a comparable number of species, but only 25% and 38% similarity during the winter and rainy cropping seasons, respectively. In the irrigated agroecosystem, the amount of seed production diversity was almost double in the winter season, compared to the rainy season. The weed seedbank diversity was low but was sensitive to cropping practices and seasons in both agroecosystems. A considerably smaller soil seedbank size in the irrigated agroecosystem (cf. dryland) was related to lowered weed seed production. The dryland agroecosystem showed a greater accumulation of the seeds of broad‐leaved weeds, whereas the irrigated agroecosystem accumulated more seeds of the grasses or sedges. About three‐fourths of the seeds during the winter season were accounted for byAnagallis arvensisandChenopodium albumin the dryland agroecosystem and byC. albumandMelilotus indicain the irrigated agroecosystem. However, during the rainy season,Ammannia baccifera,Echinochloa colonaandCyperus rotundusdominated in both agroecosystems. The changes in the weed seed bank and its diversity are mainly attributed to differences in water management, which tends to reduce species diversity, especially at a lower depth, but leads to the dominance of some potentially noxious weeds (e.g.Phalaris minorandM. indica). Approximately double the soil seedbank size and a greater diversity at a lower depth might indicate an adaptive mechanism in the storage of weed seeds in the dryland agroecosystem.
Bandgaps of Two-Dimensional Phononic Crystals With Sliding Interface Conditions
Authors: Li Feng-Lian , Wang Yue-Sheng , Zhang Chuanzeng , Yu Gui-Lan
Published: December 2013

In the present paper, the Dirichlet-to-Neumann map method is employed to compute the band structures of two-dimensional phononic crystals with smoothly sliding connection conditions between the matrix and the scatterers, which are composed of square or triangular lattices of circular solid cylinders in a solid matrix. The solid/solid systems of various material parameters with sliding interface conditions are considered. The influence of sliding interface conditions on the band structures is analyzed and discussed. The results show that the smoothly sliding interface condition has significant effect on the band structure.
Design and Qualification of a Parallel Robotic Platform to Assist With Beating-Heart Intracardiac Interventions
Authors: Salimi Amirhossein , Ramezanifar Amin , Mohammadpour Javad , Grigoriadis Karolos M. , Tsekos Nikolaos V.
Published: December 2013

Using robotic systems to assist with sophisticated medical interventions such as aortic valve replacement under beating heart conditions necessitates the development of dexterous manipulators to ensure a safe and reliable operation. These mechanisms should not only be capable of tracking the desired trajectories with a high level of accuracy but also need to cope with strict medical constraints such as environment compatibility, patient safety and compactness. In this paper, we propose to design and experimentally qualify a robotic platform that takes into account the aforementioned requirements. Benefiting from the features of a parallel architecture, this four degrees of freedom (DOF) magnetic resonance imaging (MRI)-compatible patient-mounted and cable-driven manipulator (ROBOCATHETER) seeks to steer cardiac catheters under beating heart condition, while suitably addressing the deficiencies that currently used manipulators vastly suffer from. In addition to the detailed description of the robot design and its dedicated power transmission system, we also present the derivation of the robot's forward and inverse kinematic equations. The control algorithm implemented for the system actuation is a varying-gain proportional-integral-derivative (PID) controller, whose tracking performance will be examined.
A Method for Measuring the Optical Efficiency of Evacuated Receivers
Authors: Kutscher Charles F. , Netter Judy C.
Published: December 2013

Evacuated receivers used with parabolic trough solar collectors can be characterized in terms of their heat loss and optical efficiency. The optical efficiency is the ratio of the energy collected to the incident solar radiation when operating at ambient temperature. If one restricts attention to the active portion of the absorber receiving incident sunlight, this is equal to the product of the transmittance of the glass cover (τ) and the absorptance of the absorber surface (α). This paper describes a new outdoor transient test method for measuring the optical efficiency. An aluminum tube is inserted into the center of the stainless steel absorber tube, and the annulus between the two tubes is filled with a measured mass of aluminum shot. The receiver is precooled and then exposed on an outdoor test rig to solar radiation. The slopes of the temperature versus time curves for the aluminum filler and the steel tube are taken during a period of steady solar radiation and near the point at which the average glass temperature is close to the average absorber temperature (i.e., when there is minimal heat loss from the absorber tube to ambient). The slopes are then used to determine the optical efficiency. This method has the advantage of using the actual solar spectrum and has an uncertainty of about ±3%, which can be improved upon if a reference receiver is used for comparison. When this method was applied to the active section of the receiver tube, measurements of an actual receiver tube yielded a τα that, to within experimental uncertainty, is consistent with the manufacturer's values of τ and α.
A Kirigami-Inspired 8R Linkage and Its Evolved Overconstrained 6R Linkages With the Rotational Symmetry of Order Two
Authors: Zhang Ketao , Dai Jian S.
Published: December 2013

This paper presents a novel metamorphic 8R linkage extracted from a kirigami-fold with pregrooved creases and two overconstrained 6R linkages evolved from the 8R linkage by taking the concept of metamorphosis in the sense of structural evolution. The geometric characteristics and the parametric constraints of the evolved 6R linkages are identified following the structural evolution of the 8R linkage. The paper reveals that the evolved 6R linkages are special line-symmetric Bricard 6R loops characterized by the rotational symmetry of order two. The joint space of the overconstrained 6R linkages is analyzed and the relationship between motion parameters of the evolved 6R linkages and reconfiguration parameters of the metamorphic 8R linkage are derived. The motion characteristics of the overconstrained 6R linkages are further verified in terms of screw theory. The bifurcation and trifurcation associated with various transitory positions of the evolved 6R linkages having distinct parametric constraints are consequently identified based on constraint analysis.
Classification of Screw Systems Composed of Three Planar Pencils of Lines for Singularity Analysis of Parallel Mechanisms1
Authors: Kong Xianwen , Johnson Andrew
Published: December 2013

Screw systems composed of (the sum of) three planar pencils of lines are closely related to the singularity analysis of a number of three-legged parallel manipulators (PMs) in which the passive joints in each leg are a spherical joint and a single-DOF (degree of freedom) kinematic joint or generalized kinematic joint. This paper systematically classifies the screw systems composed of three planar pencils of lines based on the intersection of two planar pencils of lines, the classification of screw systems of order 2, and the reciprocal screw system of the three planar pencils of lines. The classification in this paper is more comprehensive than those in the literature. The above results are illustrated using CAD figures. This work may help readers better understand the geometric characteristics of singular configurations of a number of three-legged parallel manipulators.
Real-Time Identification of Time-Varying ARMAX Systems Based on Recursive Update of Its Parameters
Authors: Seydnejad Saied Reza
Published: December 2013

A new method for identification of time-varying ARMAX systems is introduced. This method is based on expansion of time-varying parameters of the ARMAX model onto a set of basis functions. A recursive formulation for updating the coefficients of the basis functions of the time-varying parameters of the system is proposed. Similar to non-real-time basis-function methods, the proposed real-time method has the capability of tracking fast changes in the parameters of a time-varying system much better than the standard Kalman and recursive least-squares (RLS) methods. A computationally efficient version of the algorithm is also presented with a small degradation in tracking properties of the original algorithm. Selection of different types of basis functions makes the new method very flexible for different applications.
Active Control of Fluid Pressure Pulsation in Hydraulic Pipe System by Bilateral-Overflow of Piezoelectric Direct-Drive Slide Valve
Authors: Changbin Guan , Zongxia Jiao , Shuai Wu , Yaoxing Shang , Fanggang Zheng
Published: December 2013

In this paper, a novel active control of fluid pressure pulsation (ACFPP) is proposed, which meets the need of the high-pressure and high-speed hydraulic pipe system. A piezoelectric direct-drive slide valve (PDDSV) is designed and used as the active vibration absorber. Two ports of the PDDSV both connect to a bypass near the pump outlet and the other two ports both connect to the oil tank. By the bilateral-overflow through the shoulder of the PDDSV, the overflow wave generated in one cycle of spool motion can cancel two cycles of flow ripple. An adaptive-optimum control method based on the rotate-vector optimization method (RVOM) is adopted to adjust the control parameters in order to minimize the amplitude of the pressure pulsation. The biggest advantage of the proposed ACFPP is that it can eliminate the pressure pulsation when PDDSV only works at half of the pressure pulsation's frequency. The simulation and experimentation both verify the proposed ACFPP. By the proposed ACFPP, the suppression for the single-frequency component and dual-frequency components of the pressure pulsation have been both realized.
Estimation of the Order and Parameters of a Fractional Order Model From a Noisy Step Response Data1
Authors: Tavakoli-Kakhki Mahsan , Saleh Tavazoei Mohammad
Published: December 2013

This paper deals with integral based methods to estimate the order and parameters of simple fractional order models from the extracted noisy step response data of a process. This data can be obtained from both open-loop and closed-loop tests. Numerical simulation results are presented to verify the robustness of these proposed methods in the presence of the measurement noise.
The Effect of Acoustic Streaming on the Ring Area Around the Cavitation Erosion Pit
Authors: Yan Dayun , Wang Jiadao
Published: December 2013

The formation of a ring area around the cavitation erosion pit on carbon steel is due to the cavitation erosion–corrosion. For the ultrasonic irradiation in water, both the ultrasonic cavitation and the acoustic streaming are generated. Due to the oscillation of the horn, the acoustic streaming flows from the tip of the horn to the bulk water. So far, the acoustic streaming has not been considered in previous studies on the ultrasonic cavitation erosion–corrosion. This study first reveals that the acoustic streaming noticeably affects the evolution of the nascent ring area. The mean velocity of acoustic streaming is inversely proportional to the gap (H) between the tip of the horn and the surface of the specimen. When H is 65 mm and 40 mm, the corresponding ring area is mainly composed of vertical sandwich sheets. In contrast, when H is 17 mm, the corresponding ring area is mainly composed of horizontal thin sheets. This study provides a complete picture to understand the ultrasonic cavitation erosion–corrosion on carbon steel.
Harmonic Transfer Function to Measure Translational and Rotational Velocities With Continuous-Scan Laser Doppler Vibrometry
Authors: Yang Shifei , Allen Matthew S.
Published: December 2013

A laser Doppler vibrometer measures the translational velocity at a point along the direction of incident light. It has been shown that rotational velocities can also be recovered when the laser scans continuously along a short line or small circular path around that point. This work uses the harmonic transfer function to relate the measured translational and rotational velocities to the input force. With this concept, the continuous-scan approach can be combined with the conventional point-by-point scheme, acquiring three dimensional velocities under various types of excitation conditions in the same amount of time that is required for obtaining only the translational velocity. The proposed approach is validated on a downhill ski under free-free boundary conditions with a circular scan pattern. The influence of the circle size, the scan rate and the surface quality on the noise level is evaluated. It is found that the circular-scan approach provides smoother and more reliable mode shapes than the conventional point-by-point approach given appropriate parameters. Local slopes at the measurement locations are then computed from the identified rotational velocities, providing additional information for model validation and damage detection.
Investigation of Multiple Miniature Axial Fan Cooling Solutions and Thermal Modeling Approaches
Authors: Stafford Jason , Fortune Florian
Published: December 2013

This paper investigates the thermal and fluid dynamic characteristics due to multiple miniature axial fans with blade chord and span length scales less than 10 mm, impinging air onto finned surfaces. A coupled approach, utilizing both experimental and numerical techniques, has been devised to examine in detail the exit air flow interaction between cooling fans within an array. The findings demonstrate that fans positioned adjacently in an array can influence heat transfer performance both positively and negatively by up to 35% compared to an equivalent single fan—heat sink unit operating standalone. Numerical simulations have provided an insight into the flow fields generated by adjacent fans and also the air flow interaction with fixed fan motor support structures downstream. A novel experimental approach utilizing infrared thermography has been developed to locally assess the validity of the numerical models. In particular, an assessment on implementing compact lumped parameter fans and fans modeled with full geometric detail is shown for two configurations that are impinging air onto finned and flat surfaces. Overall, the study provides an insight into fan cooled heat sinks incorporating multiple miniature axial fans and general recommendations for improving current numerical modeling approaches.
Computation of Flow Through a Three-Dimensional Periodic Array of Porous Structures by a Parallel Immersed-Boundary Method
Authors: Alan Wei Zhenglun , Charlie Zheng Zhongquan , Yang Xiaofan
Published: December 2013

A parallel implementation of an immersed-boundary (IB) method is presented for low Reynolds number flow simulations in a representative elementary volume (REV) of porous media that are composed of a periodic array of regularly arranged structures. The material of the structure in the REV can be solid (impermeable) or microporous (permeable). Flows both outside and inside the microporous media are computed simultaneously by using an IB method to solve a combination of the Navier–Stokes equation (outside the microporous medium) and the Zwikker–Kosten equation (inside the microporous medium). The numerical simulation is firstly validated using flow through the REVs of impermeable structures, including square rods, circular rods, cubes, and spheres. The resultant pressure gradient over the REVs is compared with analytical solutions of the Ergun equation or Darcy–Forchheimer law. The good agreements demonstrate the validity of the numerical method to simulate the macroscopic flow behavior in porous media. In addition, with the assistance of a scientific parallel computational library, PETSc, good parallel performances are achieved. Finally, the IB method is extended to simulate species transport by coupling with the REV flow simulation. The species sorption behaviors in an REV with impermeable/solid and permeable/microporous materials are then studied.
Co-Pt core-shell nanostructured catalyst prepared by selective chemical vapor pulse deposition of Pt on Co as a cathode in polymer electrolyte fuel cells
Authors: Seo Sang-Joon , Chung Ho-Kyoon , Yoo Ji-Beom , Chae Heeyeop , Seo Seung-Woo , Min Cho Sung
Published: December 2013

A new type of PtCo/C catalyst for use as a cathode in polymer electrolyte fuel cells was prepared by selective chemical vapor pulse deposition (CVPD) of Pt on the surface of Co. The activity of the prepared catalyst for oxygen reduction was higher than that of a catalyst prepared by sequential impregnation (IMP) with the two metallic components. This catalytic activity difference occurs because the former catalyst has smaller Pt crystallites that produce stronger Pt-Co interactions and have a larger Pt surface area. Consequently, the CVPD catalyst has a great number of Co particles that are in close contact with the added Pt. The Pt surface was also electronically modified by interactions with Co, which were stronger in the CVPD catalyst than in the IMP catalyst, as indicated by X-ray diffraction, X-ray photoemission spectroscopy, and cyclic voltammetry measurements of the catalysts.
Effect of heat treatments and coatings on the outgassing rate of stainless steel chambers
Authors: Mamun Md Abdullah A. , Elmustafa Abdelmageed A. , Stutzman Marcy L. , Adderley Philip A. , Poelker Matthew
Published: December 2013

The outgassing rates of three nominally identical 304L stainless steel vacuum chambers were measured to determine the effect of chamber coatings and heat treatments. One chamber was coated with titanium nitride (TiN) and one with amorphous silicon (a-Si) immediately following fabrication. The last chamber was first tested without any coating and then coated with a-Si following a series of heat treatments. The outgassing rate of each chamber was measured at room temperatures between 15 and 30 °C following bakes at temperatures between 90 and 400 °C. Measurements for bare steel showed a significant reduction in the outgassing rate by nearly a factor of 20 after a 400 °C heat treatment (3.5 × 10−12 Torr L s−1 cm−2 prior to heat treatment, reduced to 1.7 × 10−13 Torr L s−1 cm−2 following heat treatment). The chambers that were coated with a-Si showed minimal change in outgassing rates with heat treatment, though an outgassing rate reduced by heat treatments prior to a-Si coating was successfully preserved throughout a series of bakes. The TiN coated chamber exhibited remarkably low outgassing rates, up to four orders of magnitude lower than the uncoated stainless steel, but the uncertainty in these rates is large due to the sensitivity limitations of the spinning rotor gauge accumulation measurement and the possibility of a small pump speed due to inhomogeneity in the TiN coating. The outgassing results are discussed in terms of diffusion-limited versus recombination-limited processes.
Macroscopic and nanometer scale stress measurement of Ni(Pt)Si silicide: Impact of thermal treatments ranging from millisecond to several hours
Authors: Morin Pierre Francois , Beneyton Remi , Gregoire Magali , Pofelski Alexandre , Clement Laurent , Muthukrishnan Shankar , Mayur Abhilash J.
Published: December 2013

The authors have measured and compared the stress in nickel silicide full sheet layers prepared with added platinum on (001) p-type Si wafers by using either a rapid thermal anneal (RTA) at 390 °C or a millisecond submelt laser dynamic scanning anneal (DSA) at 800 °C. The room temperature tensile stress of the silicide annealed with DSA is 1.65 GPa, whereas that of the silicide annealed with RTA at 390 °C is 800 MPa. Our analysis confirms that the origin of the stress lies in thermal expansion factors. Despite some small variations, the stress remains highly tensile in both layers after a 1 h post-treatment at 400 °C, with values of 1.4 GPa and 850 MPa for the DSA and RTA samples, respectively. The authors also performed strain measurements with dark field electron holography in the source drain region of 28 nm field complementary metal oxide semiconductor field effect transistors, under the silicide dot. They then determined the stress inside the silicide by combining the strain measurement with finite element mechanical simulations; values of 1.5 GPa and 600 MPa were found at the nanometer scale for the DSA and RTA samples, respectively, which are consistent with the macroscopic observations.
Genetic and Antigenic Typing of Seasonal Influenza Virus Breakthrough Cases from a 2008-2009 Vaccine Efficacy Trial
Authors: Durviaux Serge , Treanor John , Beran Jiri , Duval Xavier , Esen Meral , Feldman Gregory , Frey Sharon E. , Launay Odile , Leroux-Roels Geert , McElhaney Janet E. , Nowakowski Andrzej , Ruiz-Palacios Guillermo M. , van Essen Gerrit A. , Oostvogels Lidia , Devaster Jeanne-Marie , Walravens Karl
Published: December 2013

Estimations of the effectiveness of vaccines against seasonal influenza virus are guided by comparisons of the antigenicities between influenza virus isolates from clinical breakthrough cases with strains included in a vaccine. This study examined whether the prediction of antigenicity using a sequence analysis of the hemagglutinin (HA) gene-encoded HA1 domain is a simpler alternative to using the conventional hemagglutination inhibition (HI) assay, which requires influenza virus culturing. Specimens were taken from breakthrough cases that occurred in a trivalent influenza virus vaccine efficacy trial involving >43,000 participants during the 2008-2009 season. A total of 498 influenza viruses were successfully subtyped as A(H3N2) (380 viruses), A(H1N1) (29 viruses), B(Yamagata) (23 viruses), and B(Victoria) (66 viruses) from 603 PCR- or culture-confirmed specimens. Unlike the B strains, most A(H3N2) (377 viruses) and all A(H1N1) viruses were classified as homologous to the respective vaccine strains based on their HA1 domain nucleic acid sequence. HI titers relative to the respective vaccine strains and PCR subtyping were determined for 48% (182/380) of A(H3N2) and 86% (25/29) of A(H1N1) viruses. Eighty-four percent of the A(H3N2) and A(H1N1) viruses classified as homologous by sequence were matched to the respective vaccine strains by HI testing. However, these homologous A(H3N2) and A(H1N1) viruses displayed a wide range of relative HI titers. Therefore, although PCR is a sensitive diagnostic method for confirming influenza virus cases, HA1 sequence analysis appeared to be of limited value in accurately predicting antigenicity; hence, it may be inappropriate to classify clinical specimens as homologous or heterologous to the vaccine strain for estimating vaccine efficacy in a prospective clinical trial.
Estimates of Mumps Seroprevalence May Be Influenced by Antibody Specificity and Serologic Method
Authors: Latner Donald R. , McGrew Marcia , Williams Nobia J. , Sowers Sun B. , Bellini William J. , Hickman Carole J.
Published: December 2013

Neutralizing antibodies are assumed to be essential for protection against mumps virus infection, but their measurement is labor- and time-intensive. For this reason, enzyme-linked immunosorbent assays (ELISAs) are typically used to measure mumps-specific IgG levels. However, since there is poor correlation between mumps neutralization titers and ELISAs that measure the presence of mumps-specific IgG levels, ELISAs that better correlate with neutralization are needed. To address this issue, we measured mumps antibody levels by plaque reduction neutralization, by a commercial ELISA (whole-virus antigen), and by ELISAs specific for the mumps nucleoprotein and hemagglutinin. The results indicate that differences in the antibody response to the individual mumps proteins could partially explain the lack of correlation among various serologic tests. Furthermore, the data indicate that some seropositive individuals have low levels of neutralizing antibody. If neutralizing antibody is important for protection, this suggests that previous estimates of immunity based on whole-virus ELISAs may be overstated.
Genome Sequence of a Novel, Newly Identified Isolate of Guinea Pig Cytomegalovirus, the CIDMTR Strain
Authors: Schleiss Mark R. , Hernandez-Alvarado Nelmary , Ramaraj Thiruvarangan , Crow John A.
Published: December 2013

The sequence of a newly discovered isolate of guinea pig cytomegalovirus (GPCMV), the CIDMTR strain, was determined. The 232,778-nucleotide genome was generally well conserved with that of the 22122 reference strain, although some regions of substantial sequence divergence allowed annotation of strain-specific open reading frames encoding putative immune modulation gene products.
High-Quality Draft Genome Sequence of Vagococcus lutrae Strain LBD1, Isolated from the Largemouth Bass
Micropterus salmoides
Authors: Lebreton François , Valentino Michael D. , Duncan Lucile B. , Zeng Qiandong , Manson Mcguire Abigail , Earl Ashlee M. , Gilmore Michael S.
Published: December 2013

Vagococci are usually isolated from marine hosts and occasionally from endodontic infections. Using 16S rRNA gene comparison, the closest relatives are members of the genera
Enterococcus
and
Carnobacterium
. A draft sequence of
Vagococcus lutrae
was generated to clarify the relationship of
Vagococcus
to these and other related low-G+C Gram-positive bacteria.
Report of the 13th Vancomycin-Resistant Staphylococcus aureus Isolate from the United States
Authors: Limbago Brandi M. , Kallen Alexander J. , Zhu Wenming , Eggers Paula , McDougal Linda K. , Albrecht Valerie S.
Published: December 2013

Vancomycin-resistant
Staphylococcus aureus
(VRSA), an important multidrug-resistant organism of public health concern, has been infrequently identified in the United States since 2002. All previous VRSA isolates belonged to clonal complex 5, a lineage associated primarily with health care. This report describes the most recent (13th) U.S. VRSA isolate, the first to be community associated.
Diagnostic Potential and Antigenic Properties of Recombinant Tick-Borne Encephalitis Virus Subviral Particles Expressed in Mammalian Cells from Semliki Forest Virus Replicons
Authors: Levanov Lev , Kuivanen Suvi , Matveev Andrey , Swaminathan Sathyamangalam , Jääskeläinen-Hakala Anu , Vapalahti Olli
Published: December 2013

The precursor membrane envelope (prME) proteins of all three tick-borne encephalitis virus (TBEV) subtypes were produced based on expression from Semliki Forest virus (SFV) replicons transcribed from recombinant plasmids. Vero E6 cells transfected by these plasmids showed specific reactivities in immunofluorescence and immunoblot assays by monoclonal antibodies against European and Far-Eastern subtype strains of TBEV, indicating proper folding of the expressed glycoproteins. The prME glycoproteins were secreted into the cell culture supernatant, forming TBEV subviral particles of 20 to 30 nm in diameter. IgM μ-capture and IgG monoclonal antibody (MAb)-capture enzyme immunoassays (EIAs) were developed based on prME Karelia-94 (Siberian subtype) particles. Altogether, 140 human serum samples were tested using these assays, and the results were compared to those obtained with a commercial IgM EIA, an in-house μ-capture IgM assay based on baculovirus-expressed antigen, a commercial IgG EIA, and a hemagglutination inhibition test. Compared to reference enzyme-linked immunosorbent assays (ELISAs), the sensitivities of the generated μ-capture IgM SFV-prME and IgG MAb-capture SFV-prME EIAs were 97.4 to 100% and 98.7%, respectively, and the specificities of the two assays were 100%. IgM and IgG immunofluorescence assays (IFAs) were created based on Vero E6 cells transfected with the recombinant plasmid carrying the TBEV Karelia-94 prME glycoproteins. The IgM IFA was 100% concordant with the μ-capture IgM bac-prME ELISA. The IgG IFA sensitivity and specificity were 98.7% and 100%, respectively, compared to those of the commercial ELISA. In conclusion, the tests developed based on SFV replicon-driven expression of TBEV glycoproteins provide safe and robust alternatives for conducting TBEV serology.
Intermediate Susceptibility to Ciprofloxacin among Salmonella enterica Serovar Typhi Isolates in Lima, Peru
Authors: García Coralith , Lejon Veerle , Horna Gertrudis , Astocondor Lizeth , Vanhoof Raymond , Bertrand Sophie , Jacobs Jan
Published: December 2013

Thirty-three
Salmonella enterica
serovar Typhi blood isolates from Lima, Peru (2008 to 2012), were fully susceptible to trimethoprim-sulfamethoxazole, chloramphenicol, ceftriaxone, and tetracycline; 8/33 (24.2%) showed intermediate susceptibility to ciprofloxacin carrying mutations in the quinolone resistance-determining region of the
gyrA
gene (Ser83-Phe and Asp87-Asn) and in the
gyrB
gene (Ser464-Phe).
Loop-Mediated Isothermal Amplification for Rickettsia typhi (the Causal Agent of Murine Typhus): Problems with Diagnosis at the Limit of Detection
Authors: Dittrich Sabine , Castonguay-Vanier Josée , Moore Catrin E. , Thongyoo Narongchai , Newton Paul N. , Paris Daniel H.
Published: December 2013

Murine typhus is a flea-borne disease of worldwide distribution caused by
Rickettsia typhi
. Although treatment with tetracycline antibiotics is effective, treatment is often misguided or delayed due to diagnostic difficulties. As the gold standard immunofluorescence assay is imperfect, we aimed to develop and evaluate a loop-mediated isothermal amplification (LAMP) assay. LAMP assays have the potential to fulfill the WHO ASSURED criteria (
a
ffordable,
s
ensitive,
s
pecific,
u
ser friendly,
r
obust and rapid,
e
quipment free,
d
eliverable to those who need them) for diagnostic methodologies, as they can detect pathogen-derived nucleic acid with low technical expenditure. The LAMP assay was developed using samples of bacterial isolates (
n
= 41), buffy coat specimens from
R. typhi
PCR-positive Lao patients (
n
= 42), and diverse negative controls (
n
= 47). The method was then evaluated prospectively using consecutive patients with suspected scrub typhus or murine typhus (
n
= 266). The limit of detection was ∼40 DNA copies/LAMP reaction, with an analytical sensitivity of <10 DNA copies/reaction based on isolate dilutions. Despite these low cutoffs, the clinical sensitivity was disappointing, with 48% (95% confidence interval [95% CI], 32.5 to 62.7%) (specificity, 100% [95% CI, 100 to 100%]) in the developmental phase and 33% (95% CI, 9.2 to 56.8%) (specificity, 98.5% [95% CI, 97.0% to 100%]) in the prospective study. This low diagnostic accuracy was attributed to low patient
R. typhi
bacterial loads (median, 210 DNA copies/ml blood; interquartile range, 130 to 500). PCR-positive but LAMP-negative samples demonstrated significantly lower bacterial loads than LAMP-positive samples. Our findings highlight the diagnostic challenges for diseases with low pathogen burdens and emphasize the need to integrate pathogen biology with improved template production for assay development strategies.
Panton-Valentine Leukocidin-Positive Staphylococcus aureus in Ireland from 2002 to 2011: 21 Clones, Frequent Importation of Clones, Temporal Shifts of Predominant Methicillin-Resistant S. aureus Clones, and Increasing Multiresistance
Authors: Shore Anna C. , Tecklenborg Sarah C. , Brennan Gráinne I. , Ehricht Ralf , Monecke Stefan , Coleman David C.
Published: December 2013

There has been a worldwide increase in community-associated (CA) methicillin-resistantStaphylococcus aureus(MRSA) infections. CA-MRSA isolates commonly produce the Panton-Valentine leukocidin toxin encoded by thepvlgeneslukF-PVandlukS-PV. This study investigated the clinical and molecular epidemiologies ofpvl-positive MRSA and methicillin-susceptibleS. aureus(MSSA) isolates identified by the Irish National MRSA Reference Laboratory (NMRSARL) between 2002 and 2011. Allpvl-positive MRSA (n= 190) and MSSA (n= 39) isolates underwent antibiogram-resistogram typing,spatyping, and DNA microarray profiling for multilocus sequence type, clonal complex (CC) and/or sequence type (ST), staphylococcal cassette chromosomemectype assignment, and virulence and resistance gene detection. Where available, patient demographics and clinical data were analyzed. The prevalence ofpvl-positive MRSA increased from 0.2% to 8.8%, and that ofpvl-positive MSSA decreased from 20% to 2.5% during the study period. Thepvl-positive MRSA and MSSA isolates belonged to 16 and 5 genotypes, respectively, with CC/ST8-MRSA-IV, CC/ST30-MRSA-IV, CC/ST80-MRSA-IV, CC1/ST772-MRSA-V, CC30-MSSA, CC22-MSSA, and CC121-MSSA predominating. Temporal shifts in the predominantpvl-positive MRSA genotypes and a 6-fold increase in multiresistantpvl-positive MRSA genotypes occurred during the study period. An analysis of patient data indicated thatpvl-positiveS. aureusstrains, especially MRSA strains, had been imported into Ireland several times. Two hospital and six family clusters ofpvl-positive MRSA were identified, and 70% of the patient isolates for which information was available were from patients in the community. This study highlights the increased burden and changing molecular epidemiology ofpvl-positiveS. aureusin Ireland over the last decade and the contribution of international travel to the influx of genetically diversepvl-positiveS. aureusisolates into Ireland.
Bacteremia Caused by Comamonaskerstersii in a Patient with Diverticulosis
Authors: Opota Onya , Ney Barbara , Zanetti Giorgio , Jaton Katia , Greub Gilbert , Prod'hom Guy
Published: December 2013

We report for the first time a case of bacteremia caused by
Comamonas
kerstersii
in a 65-year-old patient with sign of diverticulosis. In addition, we review the isolation of
Comamonas
sp. and related organisms in our hospital over 25 years.
Identification and Clinical Significance of Helcococcus species, with Description of Helcococcus seattlensis sp. nov. from a Patient with Urosepsis
Authors: Chow Siu-Kei , Clarridge Jill E.
Published: December 2013

Helcococcus
spp. are Gram-positive, catalase-negative, facultatively anaerobic cocci that are associated with wound and prosthetic joint infections as well bacteremia and empyema. Five
Helcococcus
spp. strains were isolated from our patient population, including 2 strains of
Helcococcus kunzii
from trauma-associated wounds, 2
Helcococcus sueciensis
strains from blood and abscess, and a novel
Helcococcus
spp. strain from blood associated with urosepsis. Based on the phenotypic and phylogenetic evidence, we propose that the unknown bacterium be classified as
Helcococcus seattlensis
sp. nov. We found that all 5 tested
Helcococcus
strains grew as satellite colonies around
Staphylococcus aureus
and, interestingly, both
H. kunzii
strains were isolated together with
S. aureus
. In addition to 16S rRNA gene sequencing, conventional methods for leucine aminopeptidase (LAP) and pyrrolidonyl arylamidase (PYR) testing can be cost-effective and efficient for differentiation of
Helcococcus
spp. from
Abiotrophia
and
Granulicatella
species. Using nonstandard methods, we found that all tested
Helcococcus
spp. had high MICs of >4/76 μg/ml for trimethoprim-sulfamethoxazole, an antibiotic commonly used to treat urinary tract infections. High MICs for erythromycin, azithromycin, and clindamycin, and intermediate to high MICs for moxifloxacin, levofloxacin, and gentamicin were also observed among the
Helcococcus
strains.
Evaluation of Three Live Attenuated H2 Pandemic Influenza Vaccine Candidates in Mice and Ferrets
Authors: Chen Grace L. , Lamirande Elaine W. , Cheng Xing , Torres-Velez Fernando , Orandle Marlene , Jin Hong , Kemble George , Subbarao Kanta
Published: December 2013

H2 influenza viruses have not circulated in humans since 1968, and therefore a significant portion of the population would be susceptible to infection should H2 influenza viruses reemerge. H2 influenza viruses continue to circulate in avian reservoirs worldwide, and these reservoirs are a potential source from which these viruses could emerge. Three reassortant cold-adapted (ca) H2 pandemic influenza vaccine candidates with hemagglutinin (HA) and neuraminidase (NA) genes derived from the wild-type A/Japan/305/1957 (H2N2) (Jap/57), A/mallard/6750/1978 (H2N2) (mal/78), or A/swine/MO/4296424/2006 (H2N3) (sw/06) viruses and the internal protein gene segments from the A/Ann Arbor/6/60 ca virus were generated by plasmid-based reverse genetics (Jap/57 ca, mal/78 ca, and sw/06 ca, respectively). The vaccine candidates exhibited the
in vitro
phenotypes of temperature sensitivity and cold adaptation and were restricted in replication in the respiratory tract of ferrets. In mice and ferrets, the vaccines elicited neutralizing antibodies and conferred protection against homologous wild-type virus challenge. Of the three candidates, the sw/06 ca vaccine elicited cross-reactive antibodies and provided significant protection against the greatest number of heterologous viruses. These observations suggest that the sw/06 ca vaccine should be further evaluated in a clinical trial as an H2 pandemic influenza vaccine candidate.

IMPORTANCE
Influenza pandemics arise when novel influenza viruses are introduced into a population with little prior immunity to the new virus and often result in higher rates of illness and death than annual seasonal influenza epidemics. An influenza H2 subtype virus caused a pandemic in 1957, and H2 viruses circulated in humans till 1968. H2 influenza viruses continue to circulate in birds, and the development of an H2 influenza vaccine candidate is therefore considered a priority in preparing for future pandemics. However, we cannot predict whether a human H2 virus will reemerge or a novel avian H2 virus will emerge. We identified three viruses as suitable candidates for further evaluation as vaccines to protect against H2 influenza viruses and evaluated the immune responses and protection that these three vaccines provided in mice and ferrets.
Vaccinia Virus Inhibits NF-κB-Dependent Gene Expression Downstream of p65 Translocation
Authors: Sumner Rebecca P. , Maluquer de Motes Carlos , Veyer David L. , Smith Geoffrey L.
Published: December 2013

The transcription factor nuclear factor kappa light-chain enhancer of activated B cells (NF-κB) plays a critical role in host defense against viral infection by inducing the production of proinflammatory mediators and type I interferon. Consequently, viruses have evolved many mechanisms to block its activation. The poxvirus vaccinia virus (VACV) encodes numerous inhibitors of NF-κB activation that target multiple points in the signaling pathway. A derivative of VACV strain Copenhagen, called vv811, lacking 55 open reading frames in the left and right terminal regions of the genome was reported to still inhibit NF-κB activation downstream of tumor necrosis factor alpha (TNF-α) and interleukin-1β (IL-1β), suggesting the presence of one or more additional inhibitors. In this study, we constructed a recombinant vv811 lacking the recently described NF-κB inhibitor A49 (vv811ΔA49), yielding a virus that lacked all currently described inhibitors downstream of TNF-α and IL-1β. Unlike vv811, vv811ΔA49 no longer inhibited degradation of the phosphorylated inhibitor of κBα and p65 translocated into the nucleus. However, despite this translocation, vv811ΔA49 still inhibited TNF-α- and IL-1β-induced NF-κB-dependent reporter gene expression and the transcription and production of cytokines induced by these agonists. This inhibition did not require late viral gene expression. These findings indicate the presence of another inhibitor of NF-κB that is expressed early during infection and acts by a novel mechanism downstream of p65 translocation into the nucleus.
Rotavirus Infection Increases Intestinal Motility but Not Permeability at the Onset of Diarrhea
Authors: Istrate Claudia , Hagbom Marie , Vikström Elena , Magnusson Karl-Eric , Svensson Lennart
Published: December 2013

The disease mechanisms associated with onset and secondary effects of rotavirus (RV) diarrhea remain to be determined and may not be identical. In this study, we investigated whether onset of RV diarrhea is associated with increased intestinal permeability and/or motility. To study the transit time, fluorescent fluorescein isothiocyanate (FITC)-dextran was given to RV-infected adult and infant mice. Intestinal motility was also studied with an opioid receptor agonist (loperamide) and a muscarinic receptor antagonist (atropine). To investigate whether RV increases permeability at the onset of diarrhea, fluorescent 4- and 10-kDa dextran doses were given to infected and noninfected mice, and fluorescence intensity was measured subsequently in serum. RV increased transit time in infant mice. Increased motility was detected at 24 h postinfection (h p.i.) and persisted up to 72 h p.i in pups. Both loperamide and atropine decreased intestinal motility and attenuated diarrhea. Analysis of passage of fluorescent dextran from the intestine into serum indicated unaffected intestinal permeability at the onset of diarrhea (24 to 48 h p.i.). We show that RV-induced diarrhea is associated with increased intestinal motility via an activation of the myenteric nerve plexus, which in turn stimulates muscarinic receptors on intestinal smooth muscles.

IMPORTANCE
We show that RV-infected mice have increased intestinal motility at the onset of diarrhea, and that this is not associated with increased intestinal permeability. These new observations will contribute to a better understanding of the mechanisms involved in RV diarrhea.
The
MYC
,
TERT
, and
ZIC1
Genes Are Common Targets of Viral Integration and Transcriptional Deregulation in Avian Leukosis Virus Subgroup J-Induced Myeloid Leukosis
Authors: Li Yuhao , Liu Xuemei , Yang Zhen , Xu Chenggang , Liu Di , Qin Jianru , Dai Manman , Hao Jianyong , Feng Min , Huang Xiaorong , Tan Liqiang , Cao Weisheng , Liao Ming
Published: December 2013

The integration of retroviruses into the host genome following nonrandom genome-wide patterns may lead to the deregulation of gene expression and oncogene activation near the integration sites. Slow-transforming retroviruses have been widely used to perform genetic screens for the identification of genes involved in cancer. To investigate the involvement of avian leukosis virus subgroup J (ALV-J) integration in myeloid leukosis (ML) in chickens, we utilized an ALV-J insertional identification platform based on hybrid capture target enrichment and next-generation sequencing (NGS). Using high-definition mapping of the viral integration sites in the chicken genome, 241 unique insertion sites were obtained from six different ALV-J-induced ML samples. On the basis of previous statistical definitions,
MYC
,
TERT
, and
ZIC1
genes were identified as common insertion sites (CIS) of provirus integration in tumor cells; these three genes have previously been shown to be involved in the malignant transformation of different human cell types. Compared to control samples, the expression levels of all three CIS genes were significantly upregulated in chicken ML samples. Furthermore, they were frequently, but not in all field ML cases, deregulated at the mRNA level as a result of ALV-J infection. Our findings contribute to the understanding of the relationship between multipathotypes associated with ALV-J infection and the molecular background of tumorigenesis.

IMPORTANCE
ALV-Js have been successfully eradicated from chicken breeding flocks in the poultry industries of developed countries, and the control and eradication of ALV-J in China are now progressing steadily. To further study the pathogenesis of ALV-J infections, it will be necessary to elucidate the
in vivo
viral integration and tumorigenesis mechanism. In this study, 241 unique insertion sites were obtained from six different ALV-J-induced ML samples. In addition,
MYC
,
TERT
, and
ZIC1
genes were identified as the CIS of ALV-J in tumor cells, which might be a putative “driver” for the activation of the oncogene. In addition, the CIS genes showed deregulated expression compared to nontumor samples. These results have potentially important implications for the mechanism of viral carcinogenesis.
Identifying Recombination Hot Spots in the HIV-1 Genome
Authors: Smyth Redmond P. , Schlub Timothy E. , Grimm Andrew J. , Waugh Caryll , Ellenberg Paula , Chopra Abha , Mallal Simon , Cromer Deborah , Mak Johnson , Davenport Miles P.
Published: December 2013

HIV-1 infection is characterized by the rapid generation of genetic diversity that facilitates viral escape from immune selection and antiretroviral therapy. Despite recombination's crucial role in viral diversity and evolution, little is known about the genomic factors that influence recombination between highly similar genomes. In this study, we use a minimally modified full-length HIV-1 genome and high-throughput sequence analysis to study recombination in
gag
and
pol
in T cells. We find that recombination is favored at a number of recombination hot spots, where recombination occurs six times more frequently than at corresponding cold spots. Interestingly, these hot spots occur near important features of the HIV-1 genome but do not occur at sites immediately around protease inhibitor or reverse transcriptase inhibitor drug resistance mutations. We show that the recombination hot and cold spots are consistent across five blood donors and are independent of coreceptor-mediated entry. Finally, we check common experimental confounders and find that these are not driving the location of recombination hot spots. This is the first study to identify the location of recombination hot spots between two similar viral genomes with great statistical power and under conditions that closely reflect natural recombination events among HIV-1 quasispecies.

IMPORTANCE
The ability of HIV-1 to evade the immune system and antiretroviral therapy depends on genetic diversity within the viral quasispecies. Retroviral recombination is an important mechanism that helps to generate and maintain this genetic diversity, but little is known about how recombination rates vary within the HIV-1 genome. We measured recombination rates in
gag
and
pol
and identified recombination hot and cold spots, demonstrating that recombination is not random but depends on the underlying gene sequence. The strength and location of these recombination hot and cold spots can be used to improve models of viral dynamics and evolution, which will be useful for the design of robust antiretroviral therapies.