bluuebunny/crossref_metadata_2025 huggingface dataset:
Soft Particle-Induced Magnetic Erasure Without Physical Damage to the Media
Authors: Roy M. , Brand J. L.
Published: September 2007

With ever increasing areal density, interactions of particles with a head-disk interface become an ever more important factor impacting the drive reliability. Although particles trapped between the head and the disk could induce mechanical damage to the media resulting in permanent loss of data, data loss has also been observed without any obvious signs of physical damage to the media. We devised a component-level test to study this mode of data erasure on both glass and aluminium media. Our data indicate that the frictional heating associated with contact force between the particle and the disk could lead to permanent loss of data. In addition, we performed investigations to study the impact of air bearing design features, load/unload mechanism, and particle number density on the head disk interface.
Rolling of an Elastic Ellipsoid Upon an Elastic-Plastic Flat
Authors: Nélias Daniel , Antaluca Eduard , Boucly Vincent
Published: September 2007

The paper presents a numerical analysis of the rolling contact between an elastic ellipsoid and an elastic-plastic flat. Numerical simulations have been performed with the help of a contact solver called Plast-Kid®, with an algorithm based on an integral formulation or semi-analytical method. The application of both the conjugate gradient method and the discrete convolution and fast Fourier transform technique allows keeping the computing time reasonable when performing transient 3D simulations while solving the contact problem and calculating the subsurface stress and strain states. The effects of the ellipticity ratio k—ranging from 1 to 16—and of the normal load—from 4.2 GPa to 8 GPa—are investigated. The reference simulation corresponds to the rolling of a ceramic ball on a steel plate made of an AISI 52100 bearing steel under a load of 5.7 GPa. The results that are presented are, first, the permanent deformation of the surface and, second, the contact pressure distribution, the von Mises stress field, the hydrostatic pressure, and the equivalent plastic strain state within the elastic-plastic body. A comparison with an experimental surface deformation profile is also given to validate the theoretical background and the numerical procedure.
Ball Motion and Sliding Friction in a Four-Contact-Point Ball Bearing
Authors: Leblanc Alexandre , Nelias Daniel
Published: September 2007

An analysis of double arched ball bearing, which considers centrifugal forces and gyroscopic effects, is performed. Based on operating conditions of a five DOF inner ring and Coulomb friction model, the conventional bearing theory is extended from two to three or four-contact points. The commonly used control criterion of ball bearing by the inner or outer raceway is debatable and is known to fit with difficulty with experimental data. In addition, when more than two-contact points are involved, it becomes obsolete. The paper presents a mathematical model to describe the complex ball bearing internal kinematics under the effect of the external working conditions. Lubricant thickness is taken into account in geometrical equations and the nonlinear system of this quasistatic model is solved by a Newton-Raphson method. The model is first validated through comparisons with published data for conventional or single arched ball bearings. Results are also compared to those provided by the commercial software RBL4. The analysis of a double arched ball bearing is finally performed and the complex motion of the ball highlighted.
Effects of Applied Potential on Friction of a Piezoelectric Material
Authors: Mani Saikumar , Perez Ricardo , Lee Hyungoo , Ounaies Zoubeida , Hung Wayne , Liang Hong
Published: September 2007

Effects of the piezoelectricity of polyvinylidene fluoride (PVDF) on sliding friction against itself are investigated in this research. The piezoelectricity is the response of a piezoelectric material, such as PVDF, to an applied electrical voltage in terms of stress or physical dimension. Such a response is found to influence the sliding-frictional behavior. This research is beneficial in terms of understanding fundamental friction. The applications of this research are in wide areas, such as the design of a microgripper used for surgeries, microassembly, and micromanipulation.
Soft Elastohydrodynamic Analysis of Radial Lip Seals With Deterministic Microasperities on the Shaft
Authors: Hadinata Philip C. , Stephens Lyndon Scott
Published: September 2007

A numerical analysis is conducted to investigate the elastohydrodynamic effect of deterministic microasperities on the shaft of a lip seal. Various geometries of microasperities (triangular, square, hexagonal, and circular) are put into a 100×100μm2 unit cell and are investigated using Reynolds equation. For each shape, the area fraction of the microasperity is varied between 0.2 and 0.8, and the asperity height is varied between 0.3μm and 5μm. The calculation for load capacity and friction coefficient indicates that there are values for asperity height, where the load capacity and friction coefficient are optimized. These optimum heights were reached at 1–3μm. Although the lip seal surface is considered to be smooth, reverse pumping can still be obtained using an oriented triangular design. The Couette flow rate for this asperity showed lubricant is reverted back toward the seal side 2.6 times more than using a conventional lip seal. The addition of microasperities to the shaft surface shows significant improvement in lubrication characteristics for the lip seal in the form of a simultaneous reduction in friction coefficient and increase in the reverse pumping rate.
Finite Element Solution of Inertia Influenced Flow in Thin Fluid Films
Authors: Brunetière Noël , Tournerie Bernard
Published: September 2007

The aim of this paper is to present a numerical model to compute laminar, turbulent, and transitional incompressible fluid flows in thin lubricant films where inertia effects cannot be neglected. For this purpose, an averaged inertia method is used. A numerical scheme based on the finite element method is presented to solve simultaneously the momentum and continuity equations. The numerical model is then validated by confronting it with previously published analytical, experimental, and numerical results. Particular attention is devoted to analyzing the numerical conservation of mass and momentum. The influence of mesh size on numerical precision is also analyzed. Finally, the model is applied to a misaligned hydrostatic seal. These seals operate with a substantial leakage flow, where nonlaminar phenomena occur. The influence of inertia and misalignment of the faces on the seal behavior is analyzed through a comparison with an inertialess solution. Significant differences are observed for high values of the tilt angle when the flow is nonlaminar. Inertia effects increase when the flow is laminar.
The Influence of Injection Pockets on the Performance of Tilting-Pad Thrust Bearings—Part I: Theory
Authors: Heinrichson Niels , Santos Ilmar Ferreira , Fuerst Axel
Published: September 2007

This is Part I of a two-part series of papers describing the effects of high-pressure injection pockets on the operating conditions of tilting-pad thrust bearings. In Part I a numerical model based on the Reynolds equation is developed extending the three-dimensional thermoelastohydrodynamic (TEHD) analysis of tilting-pad thrust bearings to include the effects of high-pressure injection and recesses in the bearing pads. The model is applied to the analysis of an existing bearing of large dimensions and the influence of the pocket is analyzed. In the analysis, the high-pressure oil injection used for hydrostatic jacking is turned off (i.e., only the effect of the pocket is studied). It is shown that a shallow pocket positively influences the performance of the bearing because it has characteristics similar to those of a Rayleigh-step bearing. In Part II of the paper (Heinrichson, N., Fuerst, A., and Santos, I. F., 2007, ASME J. Tribol., 129(4), pp. 904–912) measurements of pressure profiles and oil film thickness for a test-pad are compared to theoretical results. The analysis of Part II deals both with flow situations, where the high-pressure injection is turned off, as well as with situations where it is turned on for hydrostatic jacking.
Granular Collision Lubrication: Experimental Investigation and Comparison to Theory
Authors: Elkholy Karim N. , Khonsari M. M.
Published: September 2007

An experimental investigation of the friction and lift characteristics of granular lubrication is presented. Experiments are carried out to demonstrate the vertical displacement (lift) observed in an annular shear cell apparatus. Results are presented for the friction coefficient as a function of the rotational speed and the applied load for several surface roughness combinations. Simulations of the kinetic theory for the granular material are performed and compared to the experimental results. The experiments provide an evidence for the formation of granular lift between two disks undergoing sliding motion.
Plastic Deterministic Contact of Rough Surfaces
Authors: Jamari J. , de Rooij M. B. , Schipper D. J.
Published: September 2007

In this paper, a theoretical and experimental investigation is presented to study the contact behavior of the plastic contact of deterministic rough surfaces. Analyses exclude bulk deformation of the rough surface and concentrate to the contact on asperity level. Surface asperities are modeled by an array of elliptic paraboloids where the unit event of a single contact is analyzed using an elastic-plastic elliptical contact model. A new method to determine the surface topography change due to plastic deformation is presented. Results show that the theoretical model developed predicts the contact area and the deformed geometry of the rough surface very well.
A Model for Junction Growth of a Spherical Contact Under Full Stick Condition
Authors: Brizmer V. , Kligerman Y. , Etsion I.
Published: September 2007

The evolution of the contact area (junction growth) of an elastic-plastic preloaded spherical contact subjected to an additional tangential loading is investigated theoretically. The normal preloading, under full stick condition, leads to the formation of a junction that can support additional tangential load. A gradual increase of this tangential load, while the normal preload remains constant, can incept plasticity of the contact zone in case the initial normal preload was elastic or enhance an existing one, thus lowering the tangential stiffness of the junction. Finally, the tangential stiffness approaches zero, which corresponds to sliding inception (i.e., loss of stability). The evolution of the contact area during the tangential loading prior to sliding inception reveals an essential junction growth which depends on the magnitude of the normal preload. The mechanism causing this junction growth seems to be new points of the sphere surface, which originally lay outside of the initial contact area that are coming into contact with the rigid flat during the tangential loading. The theoretical results for the junction growth obtained in the present work correlate well with some limited experiments.
Piezoelectric Networks for Vibration Suppression of Mistuned Bladed Disks
Authors: Yu Hongbiao , Wang K. W.
Published: September 2007

Extensive investigations have been conducted to study the vibration localization phenomenon and the excessive forced response that can be caused by mistuning in bladed disks. Most previous researches have focused on analyzing∕predicting localization or attacking the mistuning issue via mechanical tailoring. Few have focused on developing effective vibration control methods for such systems. This study extends the piezoelectric network concept, which has been utilized for mode delocalization in periodic structures, to the control of mistuned bladed disks under engine order excitation. A piezoelectric network is synthesized and optimized to effectively suppress vibration in bladed disks. One of the merits of such an approach is that the optimum design is independent of the number of spatial harmonics, or engine orders. Local circuits are first formulated by connecting inductors and resistors with piezoelectric patches on the individual blades. Although these local circuits can function as conventional damped absorber when properly tuned, they do not perform well for bladed disks under all engine order excitations. To address this issue, capacitors are introduced to couple the individual local circuitries. Through such networking, an absorber system that is independent of the engine order can be achieved. Monte Carlo simulation is performed to investigate the effectiveness of the network for a bladed disk with a range of mistuning level of its mechanical properties. The robustness issue of the network in terms of detuning of the electric circuit parameters is also studied. Finally, negative capacitance is introduced and its effect on the performance and robustness of the network is investigated.
Vibrations and Power Flows in a Coupled Beam System
Authors: Li Wen L. , Bonilha Murilo W. , Xiao Jie
Published: September 2007

Vibrations of and power flow between coupled beams have been the subject of many investigations, and various techniques have been developed over the years. However, most of the existing methods will require a certain level of modifications or adaptations to account for the variations in the coupling and∕or boundary conditions. In this study, a general analytical method is developed for predicting the vibrations of and power flow between two-coupled beams. The coupling between the beams is generically represented by two (translational and rotational) springs of arbitrary stiffnesses. Thus, many rigid and nonrigid connectors of practical interest can be directly taken into account. In addition, because the beams are elastically restrained at each end, the current method can be universally applied to different boundary conditions by simply varying the stiffnesses of the boundary springs. Numerical results are presented to show the excellent accuracy of the proposed approach.
A Closer Look at Water-Related Geologic Activity on Mars
Authors: McEwen A. S. , Hansen C. J. , Delamere W. A. , Eliason E. M. , Herkenhoff K. E. , Keszthelyi L. , Gulick V. C. , Kirk R. L. , Mellon M. T. , Grant J. A. , Thomas N. , Weitz C. M. , Squyres S. W. , Bridges N. T. , Murchie S. L. , Seelos F. , Seelos K. , Okubo C. H. , Milazzo M. P. , Tornabene L. L. , Jaeger W. L. , Byrne S. , Russell P. S. , Griffes J. L. , Martínez-Alonso S. , Davatzes A. , Chuang F. C. , Thomson B. J. , Fishbaugh K. E. , Dundas C. M. , Kolb K. J. , Banks M. E. , Wray J. J.
Published: September 2007

Water has supposedly marked the surface of Mars and produced characteristic landforms. To understand the history of water on Mars, we take a close look at key locations with the High-Resolution Imaging Science Experiment on board the Mars Reconnaissance Orbiter, reaching fine spatial scales of 25 to 32 centimeters per pixel. Boulders ranging up to ∼2 meters in diameter are ubiquitous in the middle to high latitudes, which include deposits previously interpreted as finegrained ocean sediments or dusty snow. Bright gully deposits identify six locations with very recent activity, but these lie on steep (20° to 35°) slopes where dry mass wasting could occur. Thus, we cannot confirm the reality of ancient oceans or water in active gullies but do see evidence of fluvial modification of geologically recent mid-latitude gullies and equatorial impact craters.
Response to Comment on "Organics Captured from Comet 81P/Wild 2 by the Stardust Spacecraft"
Authors: Sandford Scott A. , Brownlee Donald E.
Published: September 2007

Caution must be taken in interpreting measurements of organics in Stardust samples. In particular, as noted in Sandford et al. and reinforced in the comment by Spencer and Zare, one component of Stardust organics, the low-mass polycyclic aromatic hydrocarbons seen diffusely along track surfaces, should be treated cautiously because they may be due to impact conversion of aerogel carbon.
Feather Quill Knobs in the Dinosaur
Velociraptor
Authors: Turner Alan H. , Makovicky Peter J. , Norell Mark A.
Published: September 2007

Some nonavian theropod dinosaurs were at least partially covered in feathers or filamentous protofeathers. However, a complete understanding of feather distribution among theropod dinosaurs is limited because feathers are typically preserved only in lagerst�tten like that of Solnhofen, Germany or Liaoning, China. Such deposits possess clear taphonomic biases toward small-bodied animals, limiting our knowledge regarding feather presence in larger members of feathered clades. We present direct evidence of feathers in Velociraptor mongoliensis based on the presence of quill knobs on the posterior forearm. This report of secondaries in a larger-bodied, derived, and clearly flightless member of a nonavian theropod clade represented by feathered relatives is a substantial contribution to our knowledge of the evolution of feathers.
Draft Genome of the Filarial Nematode ParasiteBrugia malayi
Authors: Ghedin Elodie , Wang Shiliang , Spiro David , Caler Elisabet , Zhao Qi , Crabtree Jonathan , Allen Jonathan E. , Delcher Arthur L. , Guiliano David B. , Miranda-Saavedra Diego , Angiuoli Samuel V. , Creasy Todd , Amedeo Paolo , Haas Brian , El-Sayed Najib M. , Wortman Jennifer R. , Feldblyum Tamara , Tallon Luke , Schatz Michael , Shumway Martin , Koo Hean , Salzberg Steven L. , Schobel Seth , Pertea Mihaela , Pop Mihai , White Owen , Barton Geoffrey J. , Carlow Clotilde K. S. , Crawford Michael J. , Daub Jennifer , Dimmic Matthew W. , Estes Chris F. , Foster Jeremy M. , Ganatra Mehul , Gregory William F. , Johnson Nicholas M. , Jin Jinming , Komuniecki Richard , Korf Ian , Kumar Sanjay , Laney Sandra , Li Ben-Wen , Li Wen , Lindblom Tim H. , Lustigman Sara , Ma Dong , Maina Claude V. , Martin David M. A. , McCarter James P. , McReynolds Larry , Mitreva Makedonka , Nutman Thomas B. , Parkinson John , Peregrín-Alvarez José M. , Poole Catherine , Ren Qinghu , Saunders Lori , Sluder Ann E. , Smith Katherine , Stanke Mario , Unnasch Thomas R. , Ware Jenna , Wei Aguan D. , Weil Gary , Williams Deryck J. , Zhang Yinhua , Williams Steven A. , Fraser-Liggett Claire , Slatko Barton , Blaxter Mark L. , Scott Alan L.
Published: September 2007

Parasitic nematodes that cause elephantiasis and river blindness threaten hundreds of millions of people in the developing world. We have sequenced the ∼90 megabase (Mb) genome of the human filarial parasiteBrugia malayiand predict ∼11,500 protein coding genes in 71 Mb of robustly assembled sequence. Comparative analysis with the free-living, model nematodeCaenorhabditis elegansrevealed that, despite these genes having maintained little conservation of local synteny during ∼350 million years of evolution, they largely remain in linkage on chromosomal units. More than 100 conserved operons were identified. Analysis of the predicted proteome provides evidence for adaptations ofB. malayito niches in its human and vector hosts and insights into the molecular basis of a mutualistic relationship with itsWolbachiaendosymbiont. These findings offer a foundation for rational drug design.
Inventing Johannes Müller
Authors: Nyhart Lynn K.
Published: September 2007

Müller's Lab
.
By Laura Otis
. Oxford University Press, Oxford, 2007. 336 pp. $55, £32.99. ISBN 9780195306972.

The author uses the contradictory accounts of Müller's life and research left by seven of his influential students to explore the personal, social, and political circumstances that shaped the careers of the group.
Quantum Spin Hall Insulator State in HgTe Quantum Wells
Authors: König Markus , Wiedmann Steffen , Brüne Christoph , Roth Andreas , Buhmann Hartmut , Molenkamp Laurens W. , Qi Xiao-Liang , Zhang Shou-Cheng
Published: September 2007

Recent theory predicted that the quantum spin Hall effect, a fundamentally new quantum state of matter that exists at zero external magnetic field, may be realized in HgTe/(Hg,Cd)Te quantum wells. We fabricated such sample structures with low density and high mobility in which we could tune, through an external gate voltage, the carrier conduction from n-type to p-type, passing through an insulating regime. For thin quantum wells with well width
d
< 6.3 nanometers, the insulating regime showed the conventional behavior of vanishingly small conductance at low temperature. However, for thicker quantum wells (
d
> 6.3 nanometers), the nominally insulating regime showed a plateau of residual conductance close to 2
e
2
/
h
, where
e
is the electron charge and
h
is Planck's constant. The residual conductance was independent of the sample width, indicating that it is caused by edge states. Furthermore, the residual conductance was destroyed by a small external magnetic field. The quantum phase transition at the critical thickness,
d
= 6.3 nanometers, was also independently determined from the magnetic field–induced insulator-to-metal transition. These observations provide experimental evidence of the quantum spin Hall effect.
Comparison of Phenotypically Indistinguishable but Geographically Distinct
Neisseria meningitidis
Group B Isolates in a Serum Bactericidal Antibody Assay
Authors: Findlow Jamie , Holland Ann , Andrews Nick , Weynants Vincent , Sotolongo Franklin , Balmer Paul , Poolman Jan , Borrow Ray
Published: September 2007

The “gold standard” assay for measuring serologic protection against
Neisseria meningitidis
group B (MenB) is the serum bactericidal antibody (SBA) assay. Of vital importance to the outcome of the SBA assay is the choice of the target strain(s), which is often chosen on the basis of phenotype or genotype. We therefore investigated the effect on the results produced by the SBA assay of using phenotypically indistinguishable but geographically distinct MenB isolates. Nine PorA P1.19,15 and 11 PorA P1.7-2,4 MenB isolates were incorporated into the SBA assay using human complement and were assayed against sera obtained either before or after outer membrane vesicle vaccination. Large differences in the results produced by the isolates in the SBA assay were demonstrated. These included differences as great as 5.8-fold in SBA geometric mean titers and in the proportions of subjects with SBA titers of ≥4. Ranges of as many as 9 SBA titers were achieved by individual sera across the panels of isolates. To determine the reasons for the differences observed, investigations into the expression of capsular polysaccharide, PorA, PorB, Opc, and lipooligosaccharide (LOS) and into LOS sialylation were completed. However, minor differences were found between strains, indicating similar expression and no antigen masking. These results have implications for the choice of MenB target strains for inclusion in future studies of MenB vaccines and highlight the requirement for standardization of target strains between laboratories.
Changing Molecular Epidemiology of Methicillin-Resistant
Staphylococcus aureus
in a Small Geographic Area over an Eight-Year Period
Authors: Blanc D. S. , Petignat C. , Wenger A. , Kuhn G. , Vallet Y. , Fracheboud D. , Trachsel S. , Reymond M. , Troillet N. , Siegrist H. H. , Oeuvray S. , Bes M. , Etienne J. , Bille J. , Francioli P. , Zanetti G.
Published: September 2007

The epidemiology of methicillin-resistant
Staphylococcus aureus
(MRSA) at an international level shows that most MRSA strains belong to a few pandemic clones. At the local level, a predominance of one or two clones was generally reported. However, the situation is evolving and new clones are emerging worldwide, some of them with specific biological characteristics, such as the presence of Panton-Valentine leucocidin (PVL). Understanding these changes at the local and international levels is of great importance. Our objective was to analyze the evolution of MRSA epidemiology at multiple sites on a local level (Western Switzerland) over a period of 8 years. Data were based on MRSA reports from seven sentinel laboratories and infection control programs covering different areas. Pulsed-field gel electrophoresis was used to type MRSA isolates. From 1997 to 2004, a total of 2,256 patients with MRSA were reported. Results showed the presence of four predominant clones (accounting for 86% of patients), which could be related to known international clones (Berlin, New York/Japan, Southern Germany, and Iberian clones). Within the small geographic region, the 8-year follow-up period in the different areas showed spacio-temporal differences in the relative proportions of the four clones. Other international MRSA clones, as well as clones showing genetic characteristics identical to those of community-acquired MRSA (SCC
mec
type IV and the presence of PVL genes), were also identified but presumably did not disseminate. Despite the worldwide predominance of a few MRSA clones, our data showed that at a local level, the epidemiology of MRSA might be different from one hospital to another. Moreover, MRSA clones were replaced by other emerging clones, suggesting a rapid change.
Multilocus Variable-Number Tandem-Repeat Analysis for Molecular Typing ofShigella sonnei
Authors: Liang Shiu-Yun , Watanabe Haruo , Terajima Jun , Li Chun-Chin , Liao Jui-Cheng , Tung Sheng Kai , Chiou Chien-Shun
Published: September 2007

A multilocus variable-number tandem-repeat (VNTR) analysis (MLVA) method was developed and evaluated for the subtyping ofShigella sonneiisolates. A total of 26 VNTR loci were identified by exploring the repeat sequence loci in the genomic sequences ofS. sonneistrains Ss046 and 53G and by testing 536 isolates that had previously been characterized by pulsed-field gel electrophoresis (PFGE). The discriminatory power of MLVA (Simpson's index of diversity [D], 0.9524; 95% confidence interval [CI], 0.9373 to 0.9564) for the 536 isolates was significantly higher than that of PFGE (D, 0.8882; CI, 0.8667 to 0.9097). MLVA typing with the four and eight most variable loci hadDvalues of 0.9468 and 0.9481, respectively, results approaching that of 26 loci. The usefulness of MLVA for outbreak investigation was evaluated using 151 isolates from 10 shigellosis outbreaks and 22 PFGE-indistinguishable isolates collected from nine epidemiologically unrelated events in five different countries. The evaluations indicated that MLVA was a powerful typing tool to distinguish isolates for outbreak investigation and that it exhibited a good discrimination of the 22 PFGE-indistinguishable isolates. Single-locus variants did occur during the outbreak; therefore,S. sonneiisolates with MLVA profiles differing at no more than a single locus should be considered part of the same outbreak. The present study suggests that MLVA has the potential to replace PFGE as a standard method of typingS. sonneiisolates for disease surveillance and outbreak investigation.
Capnocytophaga cynodegmi
Peritonitis in a Peritoneal Dialysis Patient
Authors: Pers Charlotte , Tvedegaard Erling , Christensen Jens Jørgen , Bangsborg Jette
Published: September 2007

The first reported case of peritonitis caused by
Capnocytophaga cynodegmi
is presented. The patient was treated with peritoneal dialysis and had contact with a cat.
C. cynodegmi
is part of the normal oral flora of dogs and cats but is very rarely isolated in clinical specimens from humans.
Identification of “
Cronobacter
” spp. (
Enterobacter sakazakii
)
Authors: Iversen Carol , Lehner Angelika , Mullane Niall , Marugg John , Fanning Séamus , Stephan Roger , Joosten Han
Published: September 2007

A taxonomic reclassification of the neonatal pathogen
Enterobacter sakazakii
to consist of five species within a new genus, “
Cronobacter
,” has recently been proposed. The correct identification of these organisms is important to clinicians. Therefore, using 312
Enterobacteriaceae
, including 210 “
Cronobacter
” strains, the reliabilities of biochemical and genetic confirmation tests were investigated. All “
Cronobacter
” isolates were positive using
dnaG
and
gluA
PCR protocols, and all expressed α-glucosidase activity. ID32E v3.0 identified 99.5% of “
Cronobacter
” isolates (as the nearest match to
E. sakazakii
).
“
Mycobacterium ulcerans
subsp.
shinshuense
” Isolated from a Skin Ulcer Lesion: Identification Based on 16S rRNA Gene Sequencing
Authors: Nakanaga Kazue , Ishii Norihisa , Suzuki Koichi , Tanigawa Kazunari , Goto Masamichi , Okabe Tsutomu , Imada Hideaki , Kodama Akemi , Iwamoto Tomotada , Takahashi Hiroshi , Saito Hajime
Published: September 2007

We describe the fourth reported case involving “
Mycobacterium ulcerans
subsp.
shinshuense
.” Compared to previous cases, the infection was more invasive with extensive ulceration from the elbow to the forearm. Definitive identification involved IS
2404
detection, 16S rRNA gene sequencing, and analysis of the 16S rRNA gene 3′-terminal region and the virulence plasmid pMUM001.
First Case of Type E Wound Botulism Diagnosed Using Real-Time PCR
Authors: Artin Ingrid , Björkman Per , Cronqvist Jonas , Rådström Peter , Holst Elisabet
Published: September 2007

Wound botulism is a growing problem among injecting drug users. The condition is often difficult to diagnose, with laboratory confirmation in only 50% of the cases. Here we present a real-time PCR-based method for the diagnosis of wound botulism caused by
Clostridium botulinum
. The assay includes an internal amplification control which is amplified simultaneously with the genes encoding neurotoxin types A, B, and E. This method was used to detect the first case of wound botulism in an injecting drug user in Sweden. In addition, to the best of our knowledge, this is the first reported case of wound botulism caused by
C. botulinum
type E.
Evaluation of a Microculture Method for Isolation of
Leishmania
Parasites from Cutaneous Lesions of Patients in Peru
Authors: Boggild Andrea K. , Miranda-Verastegui Cesar , Espinosa Diego , Arevalo Jorge , Adaui Vanessa , Tulliano Gianfranco , Llanos-Cuentas Alejandro , Low Donald E.
Published: September 2007

Traditional culture of
Leishmania
spp. is labor intensive and has poor sensitivity. We evaluated a microculture method for the diagnosis of cutaneous leishmaniasis in consecutive patients presenting to the Leishmaniasis Clinic at the Instituto de Medicina Tropical Alexander von Humboldt, Peru, for evaluation of skin lesions. Lesion aspirates were cultured in duplicate and parallel in traditional culture tubes containing modified Novy-MacNeal-Nicolle (NNN) medium or Roswell Park Memorial Institute medium 1640 with 10% fetal bovine serum (10% RPMI) and in 70-μl capillary tubes containing a mixture of lesion aspirate and 10% RPMI. For sensitivity analysis, the consensus standard was considered to be a positive result in any two of the following four tests: Giemsa-stained lesion smear, culture, kinetoplast DNA PCR, or leishmanin skin test. The outcome measures were sensitivity and time to culture positivity. Forty-five patients with 62 skin lesions were enrolled in the study, of which 53 lesions fulfilled the consensus criteria for a final diagnosis of cutaneous leishmaniasis. Of these 53 lesions, 39 were culture positive: 38 in capillary tubes, 29 in traditional culture tubes with modified NNN medium, and 19 in traditional culture tubes with 10% RPMI medium. The sensitivity of microculture was 71.7%, versus 54.7% for traditional culture with NNN (
P
, 0.038) and 35.8% with 10% RPMI (
P
, <0.001). The mean times to culture positivity were 4.2 days by microculture, 5.2 days in NNN, and 6 days in 10% RPMI (
P
, 0.009). We have demonstrated that microculture is a more sensitive and time-efficient means of isolating
Leishmania
parasites from cutaneous lesions than traditional culture.
Streptococcus agalactiae
Serotype Ib as an Agent of Meningitis in Two Adult Nonpregnant Women
Authors: Martins E. R. , Florindo C. , Martins F. , Aldir I. , Borrego M. J. , Brum L. , Ramirez M. , Melo-Cristino J.
Published: September 2007

Two temporally and geographically clustered cases of meningitis caused by
Streptococcus agalactiae
expressing the infrequent Ib serotype are reported. Characterization by pulsed-field gel electrophoresis and multilocus sequence typing revealed that the isolates were identical and represented the widely distributed ST10/ST8 lineage associated with serotype Ib.
Human Immunodeficiency Virus-Specific CD8+T-Cell Activity Is Detectable from Birth in the Majority of In Utero-Infected Infants
Authors: Thobakgale Christina F. , Ramduth Dhanwanthie , Reddy Sharon , Mkhwanazi Nompumelelo , de Pierres Chantal , Moodley Eshia , Mphatswe Wendy , Blanckenberg Natasha , Cengimbo Ayanda , Prendergast Andrew , Tudor-Williams Gareth , Dong Krista , Jeena Prakash , Kindra Gupreet , Bobat Raziya , Coovadia Hoosen , Kiepiela Photini , Walker Bruce D. , Goulder Philip J. R.
Published: September 2007

Human immunodeficiency virus (HIV)-infected infants in sub-Saharan Africa typically progress to AIDS or death by 2 years of life in the absence of antiretroviral therapy. This rapid progression to HIV disease has been related to immaturity of the adaptive immune response in infants. We screened 740 infants born to HIV-infected mothers and tracked development and specificity of HIV-specific CD8+T-cell responses in 63 HIV-infected infants identified using gamma interferon enzyme-linked immunospot assays and intracellular cytokine staining. Forty-four in utero-infected and 19 intrapartum-infected infants were compared to 45 chronically infected children >2 years of age. Seventy percent (14 of 20) in utero-infected infants tested within the first week of life demonstrated HIV-specific CD8+T-cell responses. Gag, Pol, and Nef were the principally targeted regions in chronic pediatric infection. However, Env dominated the overall response in one-third (12/36) of the acutely infected infants, compared to only 2/45 (4%) of chronically infected children (P= 0.00083). Gag-specific CD4+T-cell responses were minimal to undetectable in the first 6 months of pediatric infection. These data indicate that failure to control HIV replication in in utero-infected infants is not due to an inability to induce responses but instead suggest secondary failure of adaptive immunity in containing this infection. Moreover, the detection of virus-specific CD8+T-cell responses in the first days of life in most in utero-infected infants is encouraging for HIV vaccine interventions in infants.
A Structural Model for Duck Hepatitis B Virus Core Protein Derived by Extensive Mutagenesis
Authors: Nassal Michael , Leifer Immanuel , Wingert Ida , Dallmeier Kai , Prinz Simone , Vorreiter Jolanta
Published: September 2007

Duck hepatitis B virus (DHBV) shares many fundamental features with human HBV. However, the DHBV core protein (DHBc), forming the nucleocapsid shell, is much larger than that of HBV (HBc) and, in contrast to HBc, there is little direct information on its structure. Here we applied an efficient expression system for recombinant DHBc particles to the biochemical analysis of a large panel of mutant DHBc proteins. By combining these data with primary sequence alignments, secondary structure prediction, and three-dimensional modeling, we propose a model for the fold of DHBc. Its major features are a HBc-like two-domain structure with an assembly domain comprising the first about 185 amino acids and a C-terminal nucleic acid binding domain (CTD), connected by a morphogenic linker region that is longer than in HBc and extends into the CTD. The assembly domain shares with HBc a framework of four major α-helices but is decorated at its tip with an extra element that contains at least one helix and that is made up only in part by the previously predicted insertion sequence. All subelements are interconnected, such that structural changes at one site are transmitted to others, resulting in an unexpected variability of particle morphologies. Key features of the model are independently supported by the accompanying epitope mapping study. These data should be valuable for functional studies on the impact of core protein structure on virus replication, and some of the mutant proteins may be particularly suitable for higher-resolution structural investigations.
Monoclonal Antibodies Providing Topological Information on the Duck Hepatitis B Virus Core Protein and Avihepadnaviral Nucleocapsid Structure
Authors: Vorreiter Jolanta , Leifer Immanuel , Rösler Christine , Jackevica Ludmila , Pumpens Paul , Nassal Michael
Published: September 2007

The icosahedral capsid of duck hepatitis B virus (DHBV) is formed by a single core protein species (DHBc). DHBc is much larger than HBc from human HBV, and no high-resolution structure is available. In an accompanying study (M. Nassal, I. Leifer, I. Wingert, K. Dallmeier, S. Prinz, and J. Vorreiter, J. Virol. 81:13218-13229, 2007), we used extensive mutagenesis to derive a structural model for DHBc. For independent validation, we here mapped the epitopes of seven anti-DHBc monoclonal antibodies. Using numerous recombinant DHBc proteins and authentic nucleocapsids from different avihepadnaviruses as test antigens, plus a panel of complementary assays, particle-specific and exposed plus buried linear epitopes were revealed. These data fully support key features of the model.
A Chaperone-Activated Nonenveloped Virus Perforates the Physiologically Relevant Endoplasmic Reticulum Membrane
Authors: Rainey-Barger Emily K. , Magnuson Brian , Tsai Billy
Published: September 2007

The nonenveloped polyomavirus (Py) traffics from the plasma membrane to the endoplasmic reticulum (ER), where it penetrates the ER membrane, allowing the viral genome to reach the nucleus to cause infection. The mechanism of membrane penetration for Py, and for other nonenveloped viruses, remains poorly characterized. We showed previously that the ER chaperone ERp29 alters the conformation of Py coat protein VP1, enabling the virus to interact with membranes. Here, we developed a membrane perforation assay and showed that the ERp29-activated Py perforates the physiologically relevant ER membrane, an event that likely initiates viral penetration. Biochemical analysis revealed that the internal protein VP2 is exposed in the activated viral particle. Accordingly, we demonstrate that VP2 binds to, integrates into, and perforates the ER membrane; the other internal protein, VP3, binds to and integrates into the ER membrane but is not sufficient for perforation. Our data thus link the activity of a cellular factor on a nonenveloped virus to the membrane perforation event and identify a viral component that mediates this process.
Humanized NOD/SCID/IL2RγnullMice Transplanted with Hematopoietic Stem Cells under Nonmyeloablative Conditions Show Prolonged Life Spans and Allow Detailed Analysis of Human Immunodeficiency Virus Type 1 Pathogenesis
Authors: Watanabe Satoru , Ohta Shinrai , Yajima Misako , Terashima Kazuo , Ito Mamoru , Mugishima Hideo , Fujiwara Shigeyoshi , Shimizu Kazufumi , Honda Mitsuo , Shimizu Norio , Yamamoto Naoki
Published: September 2007

In a previous study, we demonstrated that humanized NOD/SCID/IL2Rγnull(hNOG) mice constructed with human hematopoietic stem cells (HSCs) allow efficient human immunodeficiency virus type 1 (HIV-1) infection. However, HIV-1 infection could be monitored for only 43 days in the animals due to their short life spans. By transplanting HSCs without any myeloablation methods, the mice successfully survived longer than 300 days with stable engraftment of human cells. The mice showed high viremia state for more than the 3 months examined, with systemic HIV-1 infection and gradual decrease of CD4+T cells analogous to that in humans. These capacities of the hNOG mice are very attractive for modeling mechanisms of AIDS progression and therapeutic strategy.
Cell Culture Adaptation of Hepatitis C Virus and In Vivo Viability of an Adapted Variant
Authors: Kaul Artur , Woerz Ilka , Meuleman Philip , Leroux-Roels Geert , Bartenschlager Ralf
Published: September 2007

Production of infectious hepatitis C virus in cell culture has become possible because of the unique properties of the JFH1 isolate. However, virus titers are rather low, limiting the utility of this system. Here we describe the generation of cell culture-adapted JFH1 variants yielding higher titers of infectious particles and enhanced spread of infection in cultured cells. Sequence analysis of adapted genomes revealed a complex pattern of mutations that differed in two independent experiments. Adaptive mutations were observed both in the structural and in the nonstructural regions, with the latter having the highest impact on enhancement of virus titers. The major adaptive mutation was identified in NS5A, and it enhanced titers of three intergenotypic chimeras consisting of the structural region of a genotype 1a, 1b, or 3a isolate and the remainder of the JFH1 isolate. The mutation resides at the P3 position of the NS5A-B cleavage site and slows down processing, implying that subtle differences in replication complex formation appear to determine the efficiency of virus formation. Highly adapted JFH1 viruses carrying six mutations established a robust infection in uPA-transgenic SCID mice xenografted with human hepatocytes. However, the mutation in NS5A which enhanced virus titers in cell culture the most had reverted to wild type in nearly half of the viral genomes isolated from these animals at 15 weeks postinoculation. These results argue for some level of impaired fitness of this mutant in vivo.
Epitope Determinants of a Chimpanzee Dengue Virus Type 4 (DENV-4)-Neutralizing Antibody and Protection against DENV-4 Challenge in Mice and Rhesus Monkeys by Passively Transferred Humanized Antibody
Authors: Lai Ching-Juh , Goncalvez Ana P. , Men Ruhe , Wernly Claire , Donau Olivia , Engle Ronald E. , Purcell Robert H.
Published: September 2007

The chimpanzee monoclonal antibody (MAb) 5H2 is specific for dengue virus type 4 (DENV-4) and neutralizes the virus at a high titer in vitro. The epitope detected by the antibody was mapped by sequencing neutralization escape variants of the virus. One variant contained a Lys174-Glu substitution and another contained a Pro176-Leu substitution in domain I of the DENV-4 envelope protein (E). These mutations reduced binding affinity for the antibody 18- to >100-fold. Humanized immunoglobulin G (IgG) 5H2, originally produced from an expression vector, has been shown to be a variant containing a nine-amino-acid deletion in the Fc region which completely ablates antibody-dependent enhancement of DENV replication in vitro. The variant MAb, termed IgG 5H2 ΔD, is particularly attractive for exploring its protective capacity in vivo. Passive transfer of IgG 5H2 ΔD at 20 μg/mouse afforded 50% protection of suckling mice against challenge with 25 50% lethal doses of mouse neurovirulent DENV-4 strain H241. Passive transfer of antibody to monkeys was conducted to demonstrate proof of concept for protection against DENV challenge. Monkeys that received 2 mg/kg of body weight of IgG 5H2 ΔD were completely protected against 100 50% monkey infectious doses (MID50) of DENV-4, as indicated by the absence of viremia and seroconversion. A DENV-4 escape mutant that contained a Lys174-Glu substitution identical to that found in vitro was isolated from monkeys challenged with 106MID50of DENV-4. This substitution was also present in all naturally occurring isolates belonging to DENV-4 genotype III. These studies have important implications for possible antibody-mediated prevention of DENV infection.
Association of Nef with p21-Activated Kinase 2 Is Dispensable for Efficient Human Immunodeficiency Virus Type 1 Replication and Cytopathicity in Ex Vivo-Infected Human Lymphoid Tissue
Authors: Schindler Michael , Rajan Devi , Specht Anke , Ritter Carolin , Pulkkinen Kati , Saksela Kalle , Kirchhoff Frank
Published: September 2007

Interaction of the human immunodeficiency virus type 1 (HIV-1) Nef protein with p21-activated kinase 2 (PAK2) has been proposed to play a role in T-cell activation, viral replication, apoptosis, and progression to AIDS. However, these hypotheses were based on results obtained using Nef mutants impaired in multiple functions. Recently, it was reported that Nef residue F191 is specifically involved in PAK2 binding. However, only a limited number of Nef activities were investigated in these studies. To further evaluate the role of F191 in Nef function and to elucidate the biological relevance of Nef-PAK2 interaction, we performed a comprehensive analysis of HIV-1 Nef mutants carrying F191H and F191R mutations. We found that the F191H mutation reduces and the F191R mutation disrupts the association of Nef with PAK2. Both mutants upregulated the major histocompatibility complex II (MHC-II)-associated invariant chain and downregulated CD4, MHC-I, and CD28, although with reduced efficiency for the latter. Furthermore, the F191H/R changes neither affected the levels of interleukin-2 receptor expression and apoptosis of HIV-1-infected primary T cells nor reduced Nef-mediated induction of NFAT. Unexpectedly, the F191H change markedly reduced and the F191R mutation disrupted the ability of Nef to enhance virion infectivity in P4-CCR5 indicator cells but not in TZM-bl cells or peripheral blood mononuclear cells. Most importantly, all HIV-1 Nef mutants replicated efficiently and caused CD4
+
T-cell depletion in ex vivo-infected human lymphoid tissue. Altogether, our data show that the interaction of Nef with PAK2 does not play a major role in T-cell activation, viral replication, and apoptosis.
Epitope Mapping of the Hemagglutinin Molecule of a Highly Pathogenic H5N1 Influenza Virus by Using Monoclonal Antibodies
Authors: Kaverin Nikolai V. , Rudneva Irina A. , Govorkova Elena A. , Timofeeva Tatyana A. , Shilov Aleksandr A. , Kochergin-Nikitsky Konstantin S. , Krylov Piotr S. , Webster Robert G.
Published: September 2007

We mapped the hemagglutinin (HA) antigenic epitopes of a highly pathogenic H5N1 influenza virus on the three-dimensional HA structure by characterizing escape mutants of a recombinant virus containing A/Vietnam/1203/04 (H5N1) ΔHA and neuraminidase genes in the genetic background of A/Puerto Rico/8/34 (H1N1) virus. The mutants were selected with a panel of eight anti-HA monoclonal antibodies (MAbs), seven to A/Vietnam/1203/04 (H5N1) virus and one to A/Chicken/Pennsylvania/8125/83 (H5N2) virus, and the mutants’ HA genes were sequenced. The amino acid changes suggested three MAb groups: four MAbs reacted with the complex epitope comprising parts of the antigenic site B of H3 HA and site Sa of H1 HA, two MAbs reacted with the epitope corresponding to the antigenic site A in H3 HA, and two MAbs displayed unusual behavior: each recognized amino acid changes at two widely separate antigenic sites. Five changes were detected in amino acid residues not previously reported as changed in H5 escape mutants, and four others had substitutions not previously described. The HA antigenic structure differs substantially between A/Vietnam/1203/04 (H5N1) virus and the low-pathogenic A/Mallard/Pennsylvania/10218/84 (H5N2) virus we previously characterized (N. V. Kaverin et al., J. Gen. Virol. 83:2497-2505, 2002). The hemagglutination inhibition reactions of the MAbs with recent highly pathogenic H5N1 viruses were consistent with the antigenic-site amino acid changes but not with clades and subclades based on H5 phylogenetic analysis. These results provide information on the recognition sites of the MAbs widely used to study H5N1 viruses and demonstrate the involvement of the HA antigenic sites in the evolution of highly pathogenic H5N1 viruses, findings that can be critical for characterizing pathogenesis and vaccine design.