bluuebunny/crossref_metadata_2025 huggingface dataset:
The Physical and Computer Modeling of Plastic Deformation of Low Carbon Steel in Semisolid State
Authors: Hojny Marcin , Glowacki Miroslaw
Published: September 2009

This paper reports the results of theoretical and experimental work leading to the construction of a dedicated finite element method (FEM) system allowing the computer simulation of physical phenomena accompanying the steel sample testing at temperatures that are characteristic for integrated casting and rolling of steel processes, which was equipped with graphical, database oriented pre- and postprocessing. The kernel of the system is a numerical FEM solver based on a coupled thermomechanical model with changing density and mass conservation condition given in analytical form. The system was also equipped with an inverse analysis module having crucial significance for interpretation of results of compression tests at temperatures close to the solidus level. One of the advantages of the solution is the negligible volume loss of the deformation zone due to the analytical form of mass conservation conditions. This prevents FEM variational solution from unintentional specimen volume loss caused by numerical errors, which is inevitable in cases where the condition is written in its numerical form. It is very important for the computer simulation of deformation processes to be running at temperatures characteristic of the last stage of solidification. The still existing density change in mushy steel causes volume changes comparable to those caused by numerical errors. This paper reports work concerning the adaptation of the model to simulation of plastic behavior of axial-symmetrical steel samples subjected to compression at temperature levels higher than 1400°C. The emphasis is placed on the computer aided testing procedure leading to the determination of mechanical properties of steels at temperatures that are very close to the solidus line. Example results of computer simulation using the developed system are presented as well.
On the Mechanical Role of De Novo Synthesized Elastin in the Urinary Bladder Wall
Authors: Wognum Silvia , Schmidt David E. , Sacks Michael S.
Published: September 2009

The urinary bladder wall (UBW), which is composed of smooth muscle, collagen, and elastin, undergoes profound remodeling in response to changes in mechanical loading resulting from various pathologies. In our laboratory, we have observed the production of fibrillar elastin in the extracellular matrix (ECM), which makes the UBW a particularly attractive tissue to investigate smooth muscle tissue remodeling. In the present study, we explored the mechanical role that de novo elastin fibers play in altering UBW ECM mechanical behavior using a structural constitutive modeling approach. The mechanical behavior of the collagen fiber component of the UBW ECM was determined from the biaxial stress-stretch response of normal UBW ECM, based on bimodal fiber recruitment that was motivated by the UBW’s unique collagen fiber structure. The resulting fiber ensemble model was then combined with an experimentally derived fiber angular distribution to predict the biaxial mechanical behavior of normal and the elastin-rich UBW ECM to elucidate the underlying mechanisms of elastin production. Results indicated that UBW ECM exhibited a distinct structure with highly coiled collagen fiber bundles and visible elastic fibers in the pathological situation. Elastin-rich UBW ECM had a distinct mechanical behavior with higher compliance, attributable to the indirect effect of elastin fibers contracting the collagen fiber network, resulting in a retracted unloaded reference state of the tissue. In conclusion, our results suggest that the urinary bladder responds to prolonged periods of high strain by increasing its effective compliance through the interaction between collagen and de novo synthesized elastic fibers.
Hydrostatic Pressure Stimulation of Human Mesenchymal Stem Cells Seeded on Collagen-Based Artificial Extracellular Matrices
Authors: Hess Ricarda , Douglas Timothy , Myers Kenneth A. , Rentsch Barbe , Rentsch Claudia , Worch Hartmut , Shrive Nigel G. , Hart David A. , Scharnweber Dieter
Published: September 2009

Human mesenchymal stem cells (hMSCs) from bone marrow are considered a promising cell source for bone tissue engineering applications because of their ability to differentiate into cells of the osteoblastic lineage. Mechanical stimulation is able to promote osteogenic differentiation of hMSC; however, the use of hydrostatic pressure (HP) has not been well studied. Artificial extracellular matrices containing collagen and chondroitin sulfate (CS) have promoted the expression of an osteoblastic phenotype by hMSCs. However, there has been little research into the combined effects of biochemical stimulation by matrices and simultaneous mechanical stimulation. In this study, artificial extracellular matrices generated from collagen and/or CS were coated onto polycaprolactone-co-lactide substrates, seeded with hMSCs and subjected to cyclic HP at various time points during 21 days after cell seeding to investigate the effects of biochemical, mechanical, and combined biochemical and mechanical stimulations. Cell differentiation was assessed by analyzing the expression of alkaline phosphatase (ALP) at the protein- and mRNA levels, as well as for calcium accumulation. The timing of HP stimulation affected hMSC proliferation and expression of ALP activity. HP stimulation after 6 days was most effective at promoting ALP activity. CS-containing matrices promoted the osteogenic differentiation of hMSCs. A combination of both CS-containing matrices and cyclic HP yields optimal effects on osteogenic differentiation of hMSCs on scaffolds compared with individual responses.
The nonlinear response of entangled star polymers to startup of shear flow
Authors: Tezel Amy K. , Oberhauser James P. , Graham Richard S. , Jagannathan Kamakshi , McLeish T. C. B , Leal L. Gary
Published: September 2009

We consider the response of entangled four-arm polybutadiene star solutions to steady shear and to startup of steady shear in the nonlinear shear-rate regime. Data are reported both for the shear stress, measured in a cone and plate geometry using a temperature controlled ARES rheometer, and for birefringence measured in a Couette device using two-color birefringence. These data are then compared with predictions from the Mead–Larson–Doi (MLD) and Graham, Likhtman, McLeish and Milner (GLaMM) models for linear chains, but with the reptation mechanism turned off as an “ad hoc” means of accounting for the effect of the immobile branch point in these systems. The results for both models are reasonable. However, with the Milner–McLeish model for chain length fluctuations included, the MLD model gives better results at the lowest shear rates where the deep retractions of the arms are a significant contributor to chain relaxation. On the other hand, the local implementation of convective constraint release (CCR) in the GLaMM model gives better predictions for higher shear rates between the inverse reptation and inverse Rouse times, where the CCR mechanism largely obviates any contribution of the deep arm retractions to the relaxation process.
Real-time depth sectioning: Isolating the effect of stress on structure development in pressure-driven flow
Authors: Fernandez-Ballester Lucia , Thurman Derek W. , Kornfield Julia A.
Published: September 2009

Transient structure development at a specific distance from the channel wall in a pressure-driven flow is obtained from a set of real-time measurements that integrate contributions throughout the thickness of a rectangular channel. This “depth sectioning method” retains the advantages of pressure-driven flow while revealing flow-induced structures as a function of stress. The method is illustrated by applying it to isothermal shear-induced crystallization of an isotactic polypropylene using both synchrotron x-ray scattering and optical retardance. Real-time, depth-resolved information about the development of oriented precursors reveals features that cannot be extracted from ex-situ observation of the final morphology and that are obscured in the depth-averaged in-situ measurements. For example, at 137 °C and at the highest shear stress examined (65 kPa), oriented thread-like nuclei formed rapidly, saturated within the first 7 s of flow, developed significant crystalline overgrowth during flow and did not relax after cessation of shear. At lower stresses, threads formed later and increased at a slower rate. The depth sectioning method can be applied to the flow-induced structure development in diverse complex fluids, including block copolymers, colloidal systems, and liquid-crystalline polymers.
Rheology of worm-like micelles composed of tri-block copolymer in the limit of slow dynamics
Authors: Denkova A. G. , Mendes E. , Coppens M.-O.
Published: September 2009

We study the influence of micellar kinetics on the rheological behavior of worm-like micelles composed of tri-block copolymers of ethylene oxide and propylene oxide (EO20PO70EO20) in an aqueous solution containing KCl and ethanol. The kinetics of the micelles are adjusted by changing the ethanol concentration, according to a previous study in which the lifetime of the micelles was shown to decrease exponentially with increasing ethanol concentration. At higher ethanol concentrations (15 vol % EtOH), the worm-like micelles behave like Maxwell fluids at low frequencies, but have an upturn at higher frequencies, probably due to Rouse or breathing relaxation modes. At low ethanol concentrations (5 and 8 vol % EtOH) where the lifetime of the micelles is long, the rheological behavior is clearly non-Maxwellian, revealing a spectrum of relaxation times. The slow, block copolymer dependent growth of the micelles leads to scaling of viscosity with surfactant concentration, which varies with time. In this slow breaking regime, stirring of the solutions causes an increase of the viscosity, which slowly decreases once stirring is stopped. This apparent increase of the viscosity may be induced by the linking of ring-like micelles or by the formation of clusters of worm-like micelles (non-equilibrium structures), which disassemble when stirring is stopped.
Injection of a viscoplastic material inside a tube or between two parallel disks: Conditions for wall detachment of the advancing front
Authors: Papaioannou John , Karapetsas George , Dimakopoulos Yannis , Tsamopoulos John
Published: September 2009

The injection of a viscoplastic material, driven by a constant pressure drop, inside a pipe or between two parallel coaxial disks under creeping flow conditions is examined. The transient nature of both flow arrangements requires solving a time-dependent problem and fully accounting for the advancing liquid/air interface. Material viscoplasticity is described by the Papanastasiou constitutive equation. A quasi-elliptic grid generation scheme is employed for the construction of the mesh, combined with local mesh refinement near the material front and, periodically, full mesh reconstruction. All equations are solved using the mixed finite element/Galerkin formulation coupled with the implicit Euler method. For a viscoplastic fluid, the flow field changes qualitatively from that of a Newtonian fluid because the material gets detached from the walls. For small Bingham numbers, the contact line moves in the flow direction, so that initially the flow resembles that of a Newtonian fluid, but even in that case detachment eventually occurs. The distance covered by the contact line, before detachment takes place, decreases as the Bingham number increases. For large enough Bingham numbers, the fluid may even detach from the wall without advancing appreciably. In pipe flow, when detachment occurs, unyielded material arises at the front and the flow changes into one under constant flow rate with pressure distribution that does not vary with time. In the flow between disks, it remains decelerating and the material keeps rearranging at its front because of the increased cross section through which it advances. The wall detachment we predict has been observed experimentally by Bates and Bridgwater [Chem. Eng. Sci. 55, 3003–3012 (2000)] in radial flow of pastes between two disks.
Nonlinear rheology of model comb polymers
Authors: Kapnistos M. , Kirkwood K. M. , Ramirez J. , Vlassopoulos D. , Leal L. G.
Published: September 2009

We measure the stress relaxation of linear comb polymer solutions, after a large amplitude step shear strain. We apply the time-temperature superposition principle in order to construct stress relaxation master curves that span many orders of magnitude in time and cover the entire comb relaxation from early branch retraction to backbone reptation. We find evidence of distinct relaxation processes and dynamic tube dilation that can be attributed to the architectural features of the polymer.
Nonlinearity in large amplitude oscillatory shear (LAOS) of different viscoelastic materials
Authors: Li Xin , Wang Shi-Qing , Wang Xiaorong
Published: September 2009

The present work investigates nonlinear behavior in large amplitude oscillatory shear (LAOS) of four different polymeric materials using simultaneous conventional rheometric measurements and particle-tracking velocimetric observations. In contrast to most studies in the literature that treat nonlinearity in LAOS in steady state, we emphasize by the present four examples that nonlinearity in LAOS often arise in complex fluids due to time-dependent rearrangement of their microstructures in response to LAOS. Consequently, no correlation is obvious between strain dependence of the steady-state stress response and the time-dependent characteristics of the steady-state response. For instance, a highly viscoelastic material made of nano-sized polybutadiene particles exhibits homogeneous deformation and an approximate sinusoidal wave despite strong strain softening. In a second example, a well-entangled polybutadiene solution becomes inhomogeneous over time, and the corresponding nonlinearity (i.e., strain softening) took a finite time to develop to its fullest. In the example of wall slip of a monodisperse entangled polyisoprene melt, contrary to the literature claim that even harmonics would emerge, we show that the stress response only involves odd harmonics in the absence of any edge fracture. Last, a polydisperse poly(dimethyl siloxane) melt experiences homogeneous LAOS without displaying significant higher harmonics in the absence of any edge failure. In contrast, the Fourier transform analysis shows that meniscus failure is responsible for the emergence of higher harmonics including some even ones.
The RNA-Binding Protein NANOS2 Is Required to Maintain Murine Spermatogonial Stem Cells
Authors: Sada Aiko , Suzuki Atsushi , Suzuki Hitomi , Saga Yumiko
Published: September 2009

Maintaining Germline Stem Cells

Spermatogonial stem cell pools in postnatal testes have to be maintained to continuously generate spermatozoa. It has been difficult to identify these stem cells in vivo, because of their small numbers and lack of appropriate molecular markers, but now

Sada
et al.

(p.
1394
) show that the RNA-binding protein NANOS2 is expressed in a small subset of spermatogonia that behave as self-renewing stem cells in intact testes. By a combinatorial use of loss- and gain-of-function studies, NANOS2 was found to be essential for the maintenance of the immature state of spermatogonial stem cells by supporting their self-renewing properties and by suppressing differentiation.
A G Protein–Coupled Receptor Is Essential for Schwann Cells to Initiate Myelination
Authors: Monk Kelly R. , Naylor Stephen G. , Glenn Thomas D. , Mercurio Sara , Perlin Julie R. , Dominguez Claudia , Moens Cecilia B. , Talbot William S.
Published: September 2009

Making Myelin

The myelin sheath insulates neurons and facilitates rapid axonal conduction, and its disruption is characteristic of some neurological disorders, such as multiple sclerosis. Axonal signals stimulate Schwann cells to form myelin in peripheral nerves, but the mechanism is not completely known. By characterizing a mutation identified in zebrafish,

Monk
et al.

(p.
1402
; see the Perspective by

Meijer

) show that Gpr126, a member of the G protein–coupled receptor superfamily, is essential for myelin formation. It appears that Gpr126 acts as a receptor for axonal signals to elevate cAMP levels in Schwann cells and trigger myelination.
Energy-Efficient Action Potentials in Hippocampal Mossy Fibers
Authors: Alle Henrik , Roth Arnd , Geiger Jörg R. P.
Published: September 2009

Minimizing Brain Energy Consumption

How much energy is actually required to generate neuronal activity and information processing? By combining direct recordings at physiological temperatures from mossy fiber axons in rat brain slices with modeling and simulation approaches,

Alle
et al.

(p.
1405
; see the Perspective by

Magistretti

) found that the regenerative action potentials in nonmyelinated axons of mammalian hippocampus are remarkably energy efficient. The data indicate a surprisingly minor contribution of action potentials to the entire energy expenditure of neural information processing.
Activation of Rho GTPases by DOCK Exchange Factors Is Mediated by a Nucleotide Sensor
Authors: Yang Jing , Zhang Ziguo , Roe S. Mark , Marshall Christopher J. , Barford David
Published: September 2009

Crystal Clear

Guanine nucleotide exchange factors stimulate exchange of guanine diphosphate (GDP) for guanine triphosphate (GTP) and activate small guanosine triphosphatases (GTPases) required for the regulation of many biological processes.

Yang
et al.

(p.
1398
) provide a detailed picture of the complete catalytic cycle by which a guanine nucleotide exchange factor, DOCK9, activates the small GTPase, Cdc42. A small region of DOCK9 appears to sense whether GTP or GDP is bound to Cdc42 in a mechanism that is distinct from that observed for other GTPases.
Laser Tunnel Ionization from Multiple Orbitals in HCl
Authors: Akagi H. , Otobe T. , Staudte A. , Shiner A. , Turner F. , Dörner R. , Villeneuve D. M. , Corkum P. B.
Published: September 2009

A Lower Tunnel

Among the peculiarities inherent in quantum mechanics is the ability of particles to tunnel through barriers that they lack the energy to surmount classically, as happens during radioactive decay. Strong laser fields can liberate electrons in this way from atoms and molecules.

Akagi
et al.

(p.
1364
) elegantly confirm that tunneling is not limited to the highest-energy electrons in a system by mapping the energy and momentum of both the ejected electron and positive ion produced when an intense laser pulse impinges on hydrogen chloride. When the molecule adopts specific orientations relative to the laser field, tunneling occurs from lower-lying states, as well as the highest-energy occupied orbital. This raises the possibility of tunneling microscopy capable of imaging the electronic structure of single molecules.
Potential for Wind-Generated Electricity in China
Authors: McElroy Michael B. , Lu Xi , Nielsen Chris P. , Wang Yuxuan
Published: September 2009

Blowing Away Coal

China is the world's largest carbon dioxide producer and the world's second-largest producer of electrical power, 80% of which it generates by burning coal. An affordable, carbon-free source of electrical power generation would thus constitute an important way for China to reduce its CO
2
emissions and other environmental impacts of fossil-fuel burning.

McElroy
et al.

(p.
1378
, see the cover) show that there is enough wind in China to generate electricity to supply the nation's entire projected demand for 2030 (about twice what is used now) at reasonable prices per kilowatt-hour.
A Dimeric Structure for Archaeal Box C/D Small Ribonucleoproteins
Authors: Bleichert Franziska , Gagnon Keith T. , Brown Bernard A. , Maxwell E. Stuart , Leschziner Andres E. , Unger Vinzenz M. , Baserga Susan J.
Published: September 2009

Seeing Double

A particular set of ubiquitous small (nucleolar) ribonucleoproteins are important for optimal ribosome function and protein synthesis.

Bleichert
et al.

(p.
1384
) used electron microscopy and single-particle analysis to investigate the structure of an archaeal version that contains the small RNA (sRNA) and all the associated core proteins. Unexpectedly, this ribonucleoprotein is a homodimer, formed of two sRNAs and four copies of each of the core proteins. This dimer is likely to be the enzymatically active form, as mutations disrupting di-sRNP formation inhibited activity.
Low-Cost Travel in Neurons
Authors: Magistretti Pierre J.
Published: September 2009

More precise measurements are now available for energy budgets in the brain.
Redefining Cancer Research
Authors: Alberts Bruce
Published: September 2009

Senator Ted Kennedy's recent death from malignant glioma, an incurable brain tumor, reminds us of the terrible toll that cancer takes on humanity. The United States alone experiences nearly 1.5 million new cases of cancer each year, resulting in more than 500,000 annual deaths, and about one-fourth of us will die in this way. Jim Watson, of DNA double-helix fame, argues that because of our new profound understandings of the molecular mechanisms underlying the disease, it's finally time to launch a real war on cancer.
*
I agree. But for success in such a project, we will need to expand the scope of “cancer research” funding, so as to include far more than work with cancer cells themselves.
Clothes Make the (Hu) Man
Authors: Balter Michael
Published: September 2009

Discoveries at a cave in the Republic of Georgia, reported on page
1359
of this week's issue of
Science
, suggest that humans acquired the skill to weave plant fibers into textiles more than 30,000 years ago.
Science Lags on Saving the Arctic From Oil Spills
Authors: Torrice Michael
Published: September 2009

The U.S. government is being accused of failing to design and carry out needed research.
Comparison of Real-Time PCR and Conventional Biochemical Methods for Identification of
Staphylococcus lugdunensis
Authors: Pinsky Benjamin A. , Samson Divinia , Ghafghaichi Laleh , Baron Ellen J. , Banaei Niaz
Published: September 2009

Staphylococcus lugdunensis
is an aggressive, virulent member of the coagulase-negative staphylococci (CoNS) that is responsible for severe, rapidly progressive skin and soft tissue infections and native valve endocarditis. To facilitate prompt identification and appropriate therapy, we describe here a rapid and robust multiplex real-time PCR assay that is able to definitively distinguish
S. lugdunensis
from other staphylococci. Using melting curve analysis, the assay also identifies
Staphylococcus aureus
and CoNS other than
S. lugdunensis
and determines MecA-dependent resistance to methicillin (meticillin). When applied to a panel of well-characterized staphylococcal reference strains, as well as 165 clinical isolates previously identified by conventional methods, the assay was both sensitive and specific for
S. lugdunensis
, correctly identifying the reference strain and all 47
S. lugdunensis
isolates without inappropriate amplification of other staphylococci. Furthermore, rapid biochemical identification using the WEE-TAB system to detect ornithine decarboxylase activity was found to be unsuitable as an alternative to PCR identification, displaying just 31% sensitivity and 77% specificity when tested on a subset (90 isolates) of the clinical strains. We therefore propose that this simple, accurate PCR approach will allow for the routine and timely identification of
S. lugdunensis
in the clinical microbiology laboratory.
False-Positive PCR Detection of
Tropheryma whipplei
in Cerebrospinal Fluid and Biopsy Samples from a Child with Chronic Lymphocytic Meningitis
Authors: Goyo Daniel , Camacho Ana , Gómez Carmen , de las Heras Rogelio Simón , Otero Joaquín R. , Chaves Fernando
Published: September 2009

We report the case of a teenager with chronic lymphocytic meningitis for whom
Tropheryma whipplei
16S rRNA PCR results were positive in two cerebrospinal fluid samples and one duodenal biopsy specimen. PCR targeting another specific sequence of
Tropheryma whipplei
and sequencing of the initially amplified 16S rRNA fragment did not confirm the results.
The EmsB Tandemly Repeated Multilocus Microsatellite: a New Tool To Investigate Genetic Diversity of
Echinococcus granulosus
Sensu Lato
Authors: Maillard S. , Gottstein B. , Haag K. L. , Ma S. , Colovic I. , Benchikh-Elfegoun M. C. , Knapp J. , Piarroux R.
Published: September 2009

Cystic echinococcosis (CE) is a widespread and severe zoonotic disease caused by infection with the larval stage of the eucestode
Echinococcus granulosus
sensu lato. The polymorphism exhibited by nuclear and mitochondrial markers conventionally used for the genotyping of different parasite species and strains does not reach the level necessary for the identification of genetic variants linked to restricted geographical areas. EmsB is a tandemly repeated multilocus microsatellite that proved its usefulness for the study of genetic polymorphisms within the species
E. multilocularis
, the causative agent of alveolar echinococcosis. In the present study, EmsB was used to characterize
E. granulosus
sensu lato samples collected from different host species (sheep, cattle, dromedaries, dogs, and human patients) originating from six different countries (Algeria, Mauritania, Romania, Serbia, Brazil, and the People's Republic of China). The conventional mitochondrial
cox1
and
nad1
markers identified genotypes G1, G3, G5, G6, and G7, which are clustered into three groups corresponding to the species
E. granulosus
sensu stricto,
E. ortleppi
, and
E. canadensis
. With the same samples, EmsB provided a higher degree of genetic discrimination and identified variations that correlated with the relatively small-scale geographic origins of the samples. In addition, one of the Brazilian single hydatid cysts presented a hybrid genotypic profile that suggested genetic exchanges between
E. granulosus
sensu stricto and
E. ortleppi
. In summary, the EmsB microsatellite exhibits an interesting potential for the elaboration of a detailed map of the distribution of genetic variants and therefore for the determination and tracking of the source of CE.
Infections with VIM-1 Metallo-β-Lactamase-Producing
Enterobacter cloacae
and Their Correlation with Clinical Outcome
Authors: Falcone Marco , Mezzatesta Maria Lina , Perilli Mariagrazia , Forcella Chiara , Giordano Alessandra , Cafiso Viviana , Amicosante Gianfranco , Stefani Stefania , Venditti Mario
Published: September 2009

The aim of this study was to ascertain the incidence and clinical significance of metallo-β-lactamases among
Enterobacter
strains isolated from patients with nosocomial infections. We prospectively collected data on patients with
Enterobacter
infection during a 13-month period. All of the strains were investigated for antibiotic susceptibility, the presence and expression of metallo-β-lactamases, and clonality. Of 29 infections (11 involving the urinary tract, 7 pneumonias, 3 skin/soft tissue infections, 3 intra-abdominal infections, 3 bacteremias, and 2 other infections), 7 (24%) were caused by
Enterobacter cloacae
strains harboring a
bla
VIM-1
gene associated or not with a
bla
SHV12
gene. Infections caused by VIM-1-producing strains were more frequently associated with a recent prior hospitalization (
P
= 0.006), cirrhosis (
P
= 0.03), relapse of infection (
P
< 0.001), and more prolonged duration of antibiotic therapy (
P
= 0.01) than were other infections. All of the isolates were susceptible to imipenem and meropenem and had
bla
VIM-1
preceded by a weak P1 promoter and inactivated P2 promoters. Most VIM-1-producing
Enterobacter
isolates belonged to a main clone, but four different clones were found. Multiclonal VIM-1-producing
E. cloacae
infections are difficult to diagnose due to an apparent susceptibility to various beta-lactams, including carbapenems, and are associated with a high relapse rate and a more prolonged duration of antibiotic therapy.
Phylogenetic Analysis of Human Parvovirus B19 Sequences from Eleven Different Countries Confirms the Predominance of Genotype 1 and Suggests the Spread of Genotype 3b
Authors: Hübschen Judith M. , Mihneva Zefira , Mentis Andreas F. , Schneider François , Aboudy Yair , Grossman Zehava , Rudich Hagit , Kasymbekova Kalia , Sarv Inna , Nedeljkovic Jasminka , Tahita Marc C. , Tarnagda Zekiba , Ouedraogo Jean-Bosco , Gerasimova A. G. , Moskaleva T. N. , Tikhonova Nina T. , Chitadze Nazibrola , Forbi J. C. , Faneye Adedayo O. , Otegbayo Jesse A. , Charpentier Emilie , Muller Claude P.
Published: September 2009

Phylogenetic analysis of 166 human parvovirus B19 sequences from 11 different countries attributed 91.57% to genotype 1, 5.42% to genotype 3b, and 3.01% to genotype 3a. Very similar viruses of genotype 1 circulated widely in Europe and Israel. Genotype 3b seems to show an increasing spread outside of Africa.
Comparison of a Commercial Multiplex Real-Time PCR to the Cell Cytotoxicity Neutralization Assay for Diagnosis of
Clostridium difficile
Infections
Authors: Huang Haihui , Weintraub Andrej , Fang Hong , Nord Carl Erik
Published: September 2009

A commercial multiplex real-time PCR assay (Cepheid Xpert
C. difficile
assay) for the diagnosis of
Clostridium difficile
infection was evaluated. The sensitivity and specificity of the Cepheid assay were 97.1% and 93.0% for fresh stools, using the cell cytotoxicity neutralization assay as the reference. Using PCR ribotyping as the reference for ribotype 027 strains, the corresponding figures were 100% and 98.1%, respectively.
Transmission of an Extended-Spectrum-Beta-Lactamase-Producing
Escherichia coli
(Sequence Type ST131) Strain between a Father and Daughter Resulting in Septic Shock and Emphysematous Pyelonephritis
Authors: Ender Peter T. , Gajanana Deepakraj , Johnston Brian , Clabots Connie , Tamarkin Frank J. , Johnson James R.
Published: September 2009

Probable transmission of an extended-spectrum-beta-lactamase-producing
Escherichia coli
strain (sequence type ST131) between a father and daughter was documented. The father developed severe, recurrent pyelonephritis with multiple small abscesses; the daughter later developed septic shock, bacteremia, and extensive emphysematous pyelonephritis. This multidrug-resistant
E. coli
clone appears to be highly pathogenic and transmissible.
Molecular Characteristics of German G8P[4] Rotavirus Strain GER1H-09 Suggest that a Genotyping and Subclassification Update Is Required for G8
Authors: Pietsch C. , Petersen L. , Patzer L. , Liebert U. G.
Published: September 2009

A rare G8P[4] rotavirus, designated GER1H-09, was detected in a stool sample from an infant suffering from repeated episodes of emesis for 2 days without diarrhea. Sequencing of all genomic RNA segments was performed, and complete coding sequences were determined. The VP7 amino acid sequence revealed a close phylogenetic relationship to human G8P[6] and G8P[8] isolates from Slovenia and Africa. GER1H-09 shared typical amino acid residues within variable regions VR3 to VR7 with those strains, and their subclassification as lineage G8-II rotaviruses is proposed. The variability in VR3 was identified as the likely reason for the failure in genotyping G8-II rotaviruses by commonly used multiplex PCR. Furthermore, the sequences of associated structural and nonstructural proteins showed high amino acid identities to DS-1-like rotaviruses. The genotype composition of GER1H-09 (G8-P[4]-I2-R2-C2-M2-A2-N2-T2-E2-H2) suggests the occurrence of reassortment events between G8 genotypes and human DS-1-like G2P[4] rotaviruses.
Rapid SYBR Green I and Modified Probe Real-Time Reverse Transcription-PCR Assays Identify Influenza H1N1 Viruses and Distinguish between Pandemic and Seasonal Strains
Authors: Yang Ji-Rong , Lo Je , Liu Jian-Liang , Lin Chao-Hua , Ho Yu-Lin , Chen Chun-Jung , Wu Ho-Sheng , Liu Ming-Tsan
Published: September 2009

A rapid SYBR green I real-time reverse transcription-PCR (RT-PCR) assay was developed to identify pandemic influenza H1N1 virus from clinical specimens in less than 1 h. Probe real-time RT-PCR influenza A/B, H1/H3, and swNP/swHA assays were modified into the same PCR program, which allows for rapid and simultaneous typing and subtyping of influenza viruses.
Expansion, Reexpansion, and Recall-Like Expansion of Vγ2Vδ2 T Cells in Smallpox Vaccination and Monkeypox Virus Infection
Authors: Shao Lingyun , Huang Dan , Wei Huiyong , Wang Richard C. , Chen Crystal Y. , Shen Ling , Zhang Wenhong , Jin Jialin , Chen Zheng W.
Published: September 2009

Little is known about the in vivo kinetics of T-cell responses in smallpox/monkeypox. We showed that macaque Vγ2Vδ2 T cells underwent 3-week-long expansion after smallpox vaccine immunization and displayed simple reexpansion in association with sterile anti-monkeypox virus (anti-MPV) immunity after MPV challenge. Virus-activated Vγ2Vδ2 T cells exhibited gamma interferon-producing effector function after phosphoantigen stimulation. Surprisingly, like αβ T cells, suboptimally primed Vγ2Vδ2 T cells in vaccinia virus/cidofovir-covaccinated macaques mounted major recall-like expansion after MPV challenge. Finally, Vγ2Vδ2 T cells localized in inflamed lung tissues for potential regulation. Our studies provide the first in vivo evidence that viruses, despite their inability to produce exogenous phosphoantigen, can induce expansion, reexpansion, and recall-like expansion of Vγ2Vδ2 T cells and stimulate their antimicrobial cytokine response.
Human Endogenous Retroviral Long Terminal Repeat Sequences as Cell Type-Specific Promoters in Retroviral Vectors
Authors: Schön Ulrike , Diem Olivia , Leitner Laura , Günzburg Walter H. , Mager Dixie L. , Salmons Brian , Leib-Mösch Christine
Published: September 2009

The human genome contains more than half a million human endogenous retrovirus (HERV) long terminal repeats (LTRs) that can be regarded as mobile regulatory modules. Many of these HERV LTRs have been recruited during evolution as transcriptional control elements for cellular gene expression. We have cloned LTR sequences from two HERV families, HERV-H and HERV-L, differing widely in their activity and tissue specificity into a murine leukemia virus (MLV)-based promoter conversion vector (ProCon). Various human cell lines were infected with the HERV-MLV hybrid vectors, and cell type-specific expression of the reporter gene was compared with the promoter specificity of the corresponding HERV LTRs in transient-transfection assays. Transcription start site analysis of HERV-MLV hybrid vectors revealed preferential use of the HERV promoter initiation site. Our data show that HERV LTRs function in the context of retroviral vectors in certain cell types and have the potential to be useful as cell type-specific promoters in vector construction.
Differences in the Regulatory and Functional Effects of the Us3 Protein Kinase Activities of Herpes Simplex Virus 1 and 2
Authors: Morimoto Tomomi , Arii Jun , Tanaka Michiko , Sata Tetsutaro , Akashi Hiroomi , Yamada Masao , Nishiyama Yukihiro , Uema Masashi , Kawaguchi Yasushi
Published: September 2009

Us3 protein kinases encoded by herpes simplex virus 1 (HSV-1) and 2 (HSV-2) are serine/threonine protein kinases and play critical roles in viral replication and pathogenicity in vivo. In the present study, we investigated differences in the biological properties of HSV-1 and HSV-2 Us3 protein kinases and demonstrated that HSV-2 Us3 did not have some of the HSV-1 Us3 kinase functions, including control of nuclear egress of nucleocapsids, localization of UL31 and UL34, and cell surface expression of viral envelope glycoprotein B. In agreement with the observations that HSV-2 Us3 was less important for these functions, the effect of HSV-2 Us3 kinase activity on virulence in mice following intracerebral inoculation was much lower than that of HSV-1 Us3. Furthermore, we showed that alanine substitution in HSV-2 Us3 at a site (aspartic acid at position 147) corresponding to one that can be autophosphorylated in HSV-1 Us3 abolished HSV-2 Us3 kinase activity. Thus, the regulatory and functional effects of Us3 kinase activity are different between HSV-1 and HSV-2.
Long-Term Administration of Valacyclovir Reduces the Number of Epstein-Barr Virus (EBV)-Infected B Cells but Not the Number of EBV DNA Copies per B Cell in Healthy Volunteers
Authors: Hoshino Yo , Katano Harutaka , Zou Ping , Hohman Patricia , Marques Adriana , Tyring Stephen K. , Follmann Dean , Cohen Jeffrey I.
Published: September 2009

Epstein-Barr virus (EBV) establishes a latent infection in B cells in the blood, and the latent EBV load in healthy individuals is generally stable over time, maintaining a “set point.” It is unknown if the EBV load changes after long-term antiviral therapy in healthy individuals. We treated volunteers with either valacyclovir (valaciclovir) or no antiviral therapy for 1 year and measured the amount of EBV DNA in B cells every 3 months with a novel, highly sensitive assay. The number of EBV-infected B cells decreased in subjects receiving valacyclovir (half-life of 11 months;
P
= 0.02) but not in controls (half-life of 31 years;
P
= 0.86). The difference in the slopes of the lines for the number of EBV-infected B cells over time for the valacyclovir group versus the control group approached significance (
P
= 0.054). In contrast, the number of EBV DNA copies per B cell remained unchanged in both groups (
P
= 0.62 and
P
= 0.92 for the control and valacyclovir groups, respectively). Valacyclovir reduces the frequency of EBV-infected B cells when administered over a long period and, in theory, might allow eradication of EBV from the body if reinfection does not occur.
The First Transmembrane Domain of the Hepatitis B Virus Large Envelope Protein Is Crucial for Infectivity
Authors: Lepère-Douard Charlotte , Trotard Maud , Le Seyec Jacques , Gripon Philippe
Published: September 2009

The early steps of the hepatitis B virus (HBV) life cycle are still poorly understood. Indeed, neither the virus receptor at the cell surface nor the mechanism by which nucleocapsids are delivered to the cytosol of infected cells has been identified. Extensive mutagenesis studies in pre-S1, pre-S2, and most of the S domain of envelope proteins revealed the presence of two regions essential for HBV infectivity: the 77 first residues of the pre-S1 domain and a conformational motif in the antigenic loop of the S domain. In addition, at the N-terminal extremity of the S domain, a putative fusion peptide, partially overlapping the first transmembrane (TM1) domain and preceded by a PEST sequence likely containing several proteolytic cleavage sites, was identified. Since no mutational analysis of these two motifs potentially implicated in the fusion process was performed, we decided to investigate the ability of viruses bearing contiguous deletions or substitutions in the putative fusion peptide and PEST sequence to infect HepaRG cells. By introducing the mutations either in the L and M proteins or in the S protein, we demonstrated the following: (i) that in the TM1 domain of the L protein, three hydrophobic clusters of four residues were necessary for infectivity; (ii) that the same clusters were critical for S protein expression; and, finally, (iii) that the PEST sequence was dispensable for both assembly and infection processes.
Human Papillomavirus (HPV) Type 18 Induces Extended Growth in Primary Human Cervical, Tonsillar, or Foreskin Keratinocytes More Effectively than Other High-Risk Mucosal HPVs
Authors: Lace Michael J. , Anson James R. , Klingelhutz Aloysius J. , Lee John H. , Bossler Aaron D. , Haugen Thomas H. , Turek Lubomir P.
Published: September 2009

Mucosal high-risk (HR) human papillomaviruses (HPVs) that cause cervical and other anogenital cancers also are found in ∼25% of head and neck carcinomas (HNCs), especially those arising in the oropharynx and the tonsils. While many HR HPV types are common in anogenital cancer, over 90% of HPV-positive HNCs harbor HPV type 16 (HPV-16). Using a quantitative colony-forming assay, we compared the ability of full-length mucosal HPV genomes, i.e., the low-risk HPV-11 and HR HPV-16, -18, and -31, to persist in and alter the growth of primary human keratinocytes from the foreskin, cervix, and tonsils. The HR HPV types led to the formation of growing keratinocyte colonies in culture independent of the site of epithelial origin. However, HPV-18 induced colony growth in all keratinocytes >4-fold more effectively than HPV-16 or HPV-31 and >20-fold more efficiently than HPV-11 or controls. HPV-11-transfected or control colonies failed to expand beyond 32 to 36 population doublings postexplantation. In contrast, individual HR HPV-transfected clones exhibited no apparent slowdown of growth or “crisis,” and many maintained HPV plasmid persistence beyond 60 population doublings. Keratinocyte clones harboring extrachromosomal HR HPV genomes had shorter population doubling times and formed dysplastic stratified epithelia in organotypic raft cultures, mirroring the pathological features of higher-grade intraepithelial lesions, yet did not exhibit chromosomal instability. We conclude that, in culture, the HR HPV type, rather than the site of epithelial origin of the cells, determines the efficacy of inducing continued growth of individual keratinocytes, with HPV-18 being the most aggressive mucosal HR HPV type tested.
A dynamic population-based model for the development of work-related respiratory health effects among bakery workers
Authors: Warren N , Meijster T , Heederik D , Tielemans E
Published: September 2009

Objectives:

This paper presents a dynamic population-based model for the development of sensitisation and respiratory symptoms in bakery workers. The model simulates a population of individual workers longitudinally and tracks the development of work-related sensitisation and respiratory symptoms in each worker.

Methods:

The model has three components: a multi-stage disease model describing the development of sensitisation and respiratory symptoms in each worker over time; an exposure model describing occupational exposure to flour dust and allergens; and a basic population model describing the length of a worker’s career in the bakery sector and the influx of new workers. Each worker’s disease state is modelled independently using a discrete time Markov Chain, updated yearly using each individual’s simulated exposure. A Bayesian analysis of data from a recent epidemiological study provided estimates of the yearly transition probabilities between disease states.

Results:

For non-atopic/non-sensitised workers the estimated probabilities of developing moderate (upper respiratory) symptoms and progression to severe (lower respiratory) symptoms are 0.4% (95% CI 0.3 to 0.5%) and 1.1% (95% CI 0.6 to 1.9%) per mg/m3/year of flour dust, respectively, and approximately twice these for atopic workers. The model predicts that 36% (95% CI 26 to 46%) of workers with severe symptoms are sensitised to wheat and 22% (95% CI 12 to 37%) to α-amylase. The predicted mean latency period for respiratory symptoms was 10.3 years (95% CI 8.3 to 12.3).

Conclusions:

While the model provides a valuable population-level representation of the mechanisms contributing to respiratory diseases in bakers, it was primarily developed for use in quantitative health impact assessment. Future research will use the model to evaluate a range of workplace interventions, including achievable reductions in exposure and health surveillance. The general methodology is applicable to other diseases such as chronic obstructive pulmonary disease, silicosis and musculoskeletal disorders and could be particularly valuable for forecasting changes in long latency diseases.
ON THE TFD TREATMENT OF COLLECTIVE VIBRATIONS IN HOT NUCLEI
Authors: DZHIOEV ALAN A. , VDOVIN A. I.
Published: September 2009

The approach in a theory of collective excitations in hot nuclei exploring the formalism of thermo field dynamics and the model Hamiltonian consisting of a mean field, the BCS paring interaction, and long-range particle–hole effective forces is reexamined. In contrast with earlier studies, it is found that a wave function of a thermal phonon is depended not only on the Fermi–Dirac thermal occupation numbers of the Bogoliubov quasiparticles consisting the phonon but also on the Bose thermal occupation numbers of the phonon. This strongly affects a thermal phonon coupling due to the renormalization of a phonon–phonon interaction and enlarging the number of thermal two-phonon configurations coupled with one-phonon ones. Moreover, it is shown that the formulation of the double tilde conjugation rule for fermions proposed by I. Ojima is more appropriate in the context of the present study than the original one by H. Umezawa and co-workers.
ON ASYMPTOTICS OF THREE-BODY BOUND STATE RADIAL WAVE FUNCTIONS OF HALO NUCLEI NEAR THE HYPERANGLE φ~0 AND φ~π/2 IN THE CONFIGURATION SPACE AND THREE-BODY ASYMPTOTIC NORMALIZATION FACTORS FOR 6He NUCLEUS IN THE (n+n+α)-CHANNEL
Authors: YARMUKHAMEDOV R. , UBAYDULLAEVA M. K.
Published: September 2009

Asymptotic expressions for the bound state radial partial wave functions of three-body (nnc) halo nuclei with two loosely bound valence neutrons (n) are obtained in explicit form, when the relative distance between two neutrons (r) tends to infinity and the relative distance between the center of mass of core (c) and two neutrons (ρ) is too small or vice versa. These asymptotic expressions contain a factor that can strongly influence the asymptotic values of the three-body radial wave function in the vicinity of the hyperangle of φ~0 except 0 (r→∞ and ρ is too small except 0) or φ~π/2 except π/2 (ρ→∞ and r is too small except 0) in the configuration space. The derived asymptotic forms are applied to the analysis of the asymptotic behavior of the three-body (nnα) wave function for 6He nucleus obtained by other authors on the basis of multicluster stochastic variational method using the two forms of the αN-potential. The ranges of r (or ρ) from the asymptotical regions are determined for which the agreement between the calculated wave function and the asymptotics formulae is reached. Information about the values of the three-body asymptotic normalization factors is extracted.
SOME PHENOMENA THEORETICALLY PREDICTED AND EXPLAINED BY THE TIME ANALYSIS OF THE EXPERIMENTAL DATA ON NUCLEAR PROCESSES
Authors: OLKHOVSKY V. S. , DAVYDOVSKY V. V. , DOLINSKA M. E. , DOROSHKO N. L.
Published: September 2009

The self-consistent methods in time analysis of nuclear collisions and decays are based on the properties of time as a quantum observable, canonically conjugate to energy, and the appropriate definition of mean durations of quantum collisions, the variances in their distributions, the decay functions, and the surviving functions of the meta-stable states, including radioactive and compound nuclei. Even a simplified application of these methods for the elementary study of the α-decay in the exponential-law-decay approximation resulted in the simple phenomenological method of the determination of the α-particle one-step virtual and real sojourn time inside the parent α-radioactive nucleus between the α-particle successive incoherent multiple internal reflections during the α-decay. And also the direct temporal study of the quasi-monochromatic proton scattering by 12 C and 14 N nuclei at the range of isolated resonances distorted by the nonresonant background, accompanied by the bremsstrahlung, brings to the simple revealing of the possible existence of the delay–advance phenomenon in the proton emission during scattering (in the center-of-mass system). The utilization of the self-consistent methods of time analysis to the study of high-energy nuclear reactions (near and above 0.1 GeV per nucleon in the final compound–fragment formations) resulted in the discovery of the phenomenon of time resonances (or explosions) for such formations. Some perspectives of the further study of the evident temporal phenomena in nuclear processes are also indicated.