bluuebunny/crossref_metadata_2025 huggingface dataset:
Development rate of chronic kidney disease in hepatitis C virus patients with advanced fibrosis after interferon therapy
Authors: Arase Yasuji , Suzuki Fumitaka , Kawamura Yusuke , Suzuki Yoshiyuki , Kobayashi Masahiro , Matsumoto Naoki , Akuta Norio , Sezaki Hitomi , Hosaka Tetsuya , Ogawa Kyoko , Imai Norihiro , Seko Yuya , Saito Satoshi , Ikeda Kenji , Kobayashi Mariko , Kumada Hiromitsu
Published: September 2011

Aim:  The aim of this retrospective cohort study is to assess the development incidence and predictive factors for chronic kidney disease (CKD) after the termination of interferon therapy in hepatitis C virus (HCV) positive Japanese patients with liver cirrhosis.

Methods:  A total of 650 HCV positive, liver cirrhotic patients who were treated with interferon and showed an estimated glomerular filtration rate (eGFR) of ≥60 mL/min per 1.73 m2 after the termination of interferon therapy were enrolled. CKD was defined as an eGFR of <60 mL/min per 1.73 m2. End‐stage‐CKD was defined as an eGFR of <15 mL/min/1.73 m2. The primary goal is the new development of CKD and end‐stage‐CKD.

Results:  Eighty‐five patients developed CKD, and six patients progressed to end‐stage‐CKD. The development rate of CKD was 5.2% at the 5th year, 14.5% at the 10th year and 30.6% at the 15th year. Multivariate Cox proportional hazards analysis showed that CKD occurred when patients had age increments of 10 years (hazard ratio: 2.32; 95% confidence interval [CI] 1.61–3.35; P < 0.001), eGFR decrements of 10 mL/min per 1.73 m2 (hazard ratio: 1.66; 95% CI 1.27–2.16; P < 0.001), hypertension (hazard ratio: 2.00; 95% CI 1.13–3.53; P = 0.017), diabetes (hazard ratio: 1.79; 95% CI 1.02–3.14; P = 0.042), and non‐clearance of HCV (hazard ratio: 2.67; 95% CI 1.34–5.32; P = 0.005). The development rate of end‐stage‐CKD was 0.4% at the 5th year, 1.6% at the 10th year and 2.8% at the 15th year.

Conclusions:  The annual incidence for CKD among cirrhotic patients with HCV was determined to be about 1.0–1.5%. In addition, the annual incidence for end‐stage‐CKD is one order of magnitude lower than that of CKD.
Easy‐to‐use phylogenetic analysis system for hepatitis B virus infection
Authors: Sugiyama Masaya , Inui Ayano , Shin‐I Tadasu , Komatsu Haruki , Mukaide Motokazu , Masaki Naohiko , Murata Kazumoto , Ito Kiyoaki , Nakanishi Makoto , Fujisawa Tomoo , Mizokami Masashi
Published: September 2011

Aim:  The molecular phylogenetic analysis has been broadly applied to clinical and virological study. However, the appropriate settings and application of calculation parameters are difficult for non‐specialists of molecular genetics. In the present study, the phylogenetic analysis tool was developed for the easy determination of genotypes and transmission route.

Methods:  A total of 23 patients of 10 families infected with hepatitis B virus (HBV) were enrolled and expected to undergo intrafamilial transmission. The extracted HBV DNA were amplified and sequenced in a region of the S gene.

Results:  The software to automatically classify query sequence was constructed and installed on the Hepatitis Virus Database (HVDB). Reference sequences were retrieved from HVDB, which contained major genotypes from A to H. Multiple‐alignments using CLUSTAL W were performed before the genetic distance matrix was calculated with the six‐parameter method. The phylogenetic tree was output by the neighbor‐joining method. User interface using WWW‐browser was also developed for intuitive control. This system was named as the easy‐to‐use phylogenetic analysis system (E‐PAS). Twenty‐three sera of 10 families were analyzed to evaluate E‐PAS. The queries obtained from nine families were genotype C and were located in one cluster per family. However, one patient of a family was classified into the cluster different from her family, suggesting that E‐PAS detected the sample distinct from that of her family on the transmission route.

Conclusions:  The E‐PAS to output phylogenetic tree was developed since requisite material was sequence data only. E‐PAS could expand to determine HBV genotypes as well as transmission routes.
DNA repair gene XRCC7 polymorphisms (rs#7003908 and rs#10109984) and hepatocellular carcinoma related to AFB1 exposure among Guangxi population, China
Authors: Long Xi‐Dai , Yao Jin‐Guang , Huang Yong‐Zhi , Huang Xiao‐Ying , Ban Fu‐Zhi , Yao Li‐Ming , Fan Lu‐Dan
Published: September 2011

Aim:  The X‐ray repair cross‐complementing group 7 (XRCC7) plays an important role in the repair of DNA double‐strand breaks by nonhomologous end‐joining repair (NEJR) pathway. However, the role of XRCC7 polymorphisms (rs#7003908 and rs#10109984) possibly influencing NEJR capacity in hepatocellular carcinoma (HCC) induced by aflatoxin B1 (AFB1) has not been well elaborated.

Methods:  This hospital‐based case‐control study, including 348 patients with newly diagnosed HCC and 597 controls without any evidence of liver diseases, was conducted to elucidate the association between these two polymorphisms and the risk of HCC related to AFB1 exposure among a Guangxi population from a high AFB1‐exposure area by means of TaqMAN‐polymerase chain reaction technique.

Results:  We observed that HCC patients featured higher AFB1 exposure than control group (odds ratios [OR] = 6.49 and 6.75 for exposure years and exposure levels, respectively). Furthermore, these individuals with the genotypes of XRCC7 rs#7003908 G alleles (namely XRCC7‐TG or ‐GG), compared the homozygote of XRCC7 rs#7003908 T alleles (XRCC7‐TT), faced increasing risk of HCC (OR, 3.45 and 5.04; 95% confidence intervals [CIs], 2.40–4.94 and 3.28–7.76, respectively). We also found some evidence that this polymorphism interacted with AFB1‐expousure years or levels in the process of HCC carcinogenesis. Additionally, XRCC7 rs#7003908 polymorphism was correlated with the levels of AFB1‐DNA adducts (r = 0.142, P < 0.001). XRCC7 rs#10109984 polymorphism, however, did not modify the risk of HCC related to AFB1 exposure (P > 0.05).

Conclusion:  These data suggest that XRCC7 rs#7003908 polymorphism may be one of the genetic modifiers for AFB1‐related HCC among Guangxi population.
Search for extinct aluminum‐26 and titanium‐44 in nanodiamonds from the Allende CV3 and Murchison CM2 meteorites
Authors: BESMEHN Astrid , HOPPE Peter , OTT Ulrich
Published: September 2011

Abstract– We report Mg‐Al and Ca‐Ti isotopic data for meteoritic nanodiamonds separated from the Allende CV3 and Murchison CM2 meteorites. The goal of this study was to search for excesses in 26Mg and 44Ca, which can be attributed to the in situ decay of radioactive and now extinct 26Al and 44Ti, respectively. Previous work on presolar SiC and graphite had shown that 26Al/27Al and 44Ti/48Ti ratios in presolar grains can be used to discriminate between different types of stellar sources. Aluminum and Ti concentrations are low in the meteoritic nanodiamonds of this study. Murchison nanodiamonds have higher Al and Ti concentrations than the Allende nanodiamonds. This can be attributed to contamination and the presence of presolar SiC in the Murchison nanodiamond samples. 26Mg/24Mg and 44Ca/40Ca ratios are close to normal in Allende nanodiamonds with upper limits on the initial 26Al/27Al and 44Ti/48Ti ratios of approximately 1 × 10−3. These ratios are factors of 10–1000 and, respectively, 1–1000 lower than those of presolar SiC and graphite grains from supernovae. The 26Al/27Al and 44Ti/48Ti data for nanodiamonds are compatible with an asymptotic giant branch star or solar system origin, but not with a supernova origin of a major fraction of meteoritic nanodiamonds. The latter possibility cannot be excluded, though, as the diamond separates may contain significant amounts of contaminating Al and Ti, which would lower the inferred 26Al/27Al and 44Ti/48Ti ratios considerably.
Leaf extract of Rhus verniciflua Stokes protects dopaminergic neuronal cells in a rotenone model of Parkinson's disease
Authors: Kim Seung , Park Se-Eun , Sapkota Kumar , Kim Myung-Kon , Kim Sung-Jun
Published: September 2011

Objectives

The present study investigated the neuroprotective effects of Rhus verniciflua Stokes (RVS) leaf extract on rotenone-induced apoptosis in human dopaminergic cells, SH-SY5Y.

Methods

Cells were pretreated with RVS extract for 1 h then treated with vehicle or rotenone for 24 h. Cell viability, cell cytotoxicity, cell morphology and nuclear morphology were examined by MTT assay, lactate dehydrogenase release assay, phase contrast microscopy and staining with Hoechast 33342, respectively. Reactive oxygen species were measured by 2′7′-dichlorofluorescein diacetate and fragmented DNA was observed by TUNEL assay. Mitochondrial membrane potential was determined by Rhodamine 123. Pro-apoptotic and anti-apoptotic proteins and tyrosine hydroxylase were analysed by Western blotting.

Key findings

Results showed that RVS suppressed rotenone-induced reactive oxygen species generation, cellular injury and apoptotic cell death. RVS also prevented rotenone-mediated changes in Bax/Bcl-2 levels, mitochondrial membrane potential dissipation and Caspase 3 activation. Moreover, RVS pretreatment increased the tyrosine hydroxylase levels in SH-SY5Y cells.

Conclusions

These findings demonstrate that RVS protects SH-SY5Y cells against rotenone-induced injury and suggest that RVS may have potential therapeutic value for neurodegenerative disease associated with oxidative stress.
Backbiting and bloodshed in books: Short‐term effects of reading physical and relational aggression in literature
Authors: Coyne Sarah M. , Ridge Robert , Stevens McKay , Callister Mark , Stockdale Laura
Published: September 2011

The current research consisted of two studies examining the effects of reading physical and relational aggression in literature. In both studies, participants read one of two stories (containing physical or relational aggression), and then participated in one of two tasks to measure aggression. In Study 1, participants who read the physical aggression story were subsequently more physically aggressive than those who read the relational aggression story. Conversely, in Study 2, participants who read the relational aggression story were subsequently more relationally aggressive than those who read the physical aggression story. Combined, these results show evidence for specific effects of reading aggressive content in literature.
Combining Integral Transforms and Bayesian Inference in the Simultaneous Identification of Variable Thermal Conductivity and Thermal Capacity in Heterogeneous Media
Authors: Naveira-Cotta Carolina P. , Orlande Helcio R. B. , Cotta Renato M.
Published: September 2011

This work presents the combined use of the integral transform method, for the direct problem solution, and of Bayesian inference, for the inverse problem analysis, in the simultaneous estimation of spatially variable thermal conductivity and thermal capacity for one-dimensional heat conduction within heterogeneous media. The direct problem solution is analytically obtained via integral transforms and the related eigenvalue problem is solved by the generalized integral transform technique (GITT), offering a fast, precise, and robust solution for the transient temperature field. The inverse problem analysis employs a Markov chain Monte Carlo (MCMC) method, through the implementation of the Metropolis-Hastings sampling algorithm. Instead of seeking the functions estimation in the form of local values for the thermal conductivity and capacity, an alternative approach is employed based on the eigenfunction expansion of the thermophysical properties themselves. Then, the unknown parameters become the corresponding series coefficients for the properties eigenfunction expansions. Simulated temperatures obtained via integral transforms are used in the inverse analysis, for a prescribed concentration distribution of the dispersed phase in a heterogeneous media such as particle filled composites. Available correlations for the thermal conductivity and theory of mixtures relations for the thermal capacity are employed to produce the simulated results with high precision in the direct problem solution, while eigenfunction expansions with reduced number of terms are employed in the inverse analysis itself, in order to avoid the inverse crime. Gaussian distributions were used as priors for the parameter estimation procedure. In addition, simulated results with different randomly generated errors were employed in order to test the inverse analysis robustness.
Mechanical Properties of Titania-Doped Yttria Stabilized Zirconia (TiYSZ) for Use as Thermal Barrier Coating (TBC)
Authors: Kibsey M. , Romualdez J. , Huang X. , Kearsey R. , Yang Q.
Published: September 2011

Representative samples of yttria stabilized zirconia (7YSZ) co-doped with varying concentrations of TiO2 were fabricated using plasma spraying. Samples were sintered in order to minimize porosity and to simulate the bulk material properties. After sintering, porosity levels of less than 1.25% were achieved. Both as-sprayed and sintered samples with 5, 10 and 15 wt% TiO2 addition levels were microstructurally characterized using SEM, XRD and optical image analysis methods. Vickers hardness, Young’s modulus, and fracture toughness were measured using nano and macroindentation methods. Microstructural analysis revealed that sintering of the TiO2 doped samples was required to achieve a homogeneous composition distribution, with TiO2 predominantly residing in solid solution within the ZrO2 matrix. Sintering for 325 hs at 1200 °C resulted in sufficient diffusion of TiO2 into the 7YSZ. The addition of TiO2 stabilized more tetragonal phase as revealed by XRD measurement. Sintering also showed significant improvements in fracture toughness in all co-doped samples. Fracture toughness values calculated using load-independent equations provided a clear trend in fracture toughness improvement with TiO2 addition. Ferroelastic toughening of the tetragonal phase was believed to have played an effect. There was also a reduction in monoclinic phase content with TiO2 addition, which may have limited microcrack formation and consequently increased the fracture toughness. With the addition of 10 wt% TiO2, the fracture toughness was improved by over 50%; however, this improvement started to decline at 15 wt% TiO2 addition. Volumetric porosity measurements also revealed significant improvements in fracture toughness with respect to lowering the porosity content as observed in all sintered samples.
Combined Radiation-Evaporation Model of a Liquid Droplet Layer in Space
Authors: Ye Hong , Ma Yu-Long
Published: September 2011

Assuming that the droplet layer is a uniform medium, an evaporation intensity analogous to radiation intensity was defined based on an analysis of vapor molecule transfer characteristics in the droplet layer. An evaporation transfer equation was then established, from which a one-dimensional evaporative mass flux expression was obtained and combined with the radiation heat transfer model. The combined radiation-evaporation model was used to analyze the influence of the exit temperature and the optical thickness of the droplet layer on temperature distribution, evaporation loss rate, and system lifetime. In the case of a certain droplet diameter and a small optical thickness (κD≤1), the numerical results show that temperature decreases approximately linearly with layer length. The evaporation loss rate increases as the exit temperature and optical thickness increase, and the main contribution to the evaporation loss rate comes from the high temperature portion of the liquid layer near the exit of the liquid generator, i.e., the evaporation loss rate increases rapidly in a short length of the liquid droplet layer and approaches a stable value as the length reaches a certain value. With the same working fluid mass overloading proportion of the droplet layer, the system lifetime is mainly determined by the exit temperature of the liquid droplet layer. For example, if the exit temperature decreases from 320 to 310 K, the system lifetime increases by approximately three times. However, system lifetime has a weak relationship with optical thickness.
Nucleation delay in atomic layer deposition on a thin organic layer and the role of reaction thermochemistry
Authors: Hughes Kevin J. , Engstrom James R.
Published: September 2011

The atomic layer deposition (ALD) of a series of inorganic thin films on an interfacial organic layer has been examined, focusing on the existence of a delay in thin film nucleation and its dependence on the chemistry of each ALD reaction. The inorganic thin films examined were Al2O3, HfO2, Ta2O5, and TaNx, while the organic layer was a thin (∼5 Å thick) film of poly(ethylene imine), or PEI, on SiO2. The early stages (<50 ALD cycles) of inorganic thin film growth in each case have been characterized using a combination of surface-sensitive techniques including ellipsometry, x-ray photoelectron spectroscopy, and atomic force microscopy. PEI has the effect of attenuating growth to different degrees depending on the subsequently grown ALD thin film, leading to no attenuation of growth for Al2O3, but significant incubation periods, in increasing order, for Ta2O5, HfO2 and TaNx. Angle-resolved x-ray photoelectron spectroscopy of an Al2O3 thin film deposited on PEI|SiO2 demonstrates that, in this case, the PEI thin film is buried between the Al2O3 thin film and the SiO2 substrate, with no significant decrease in the density of nitrogen from the as deposited PEI film. Results from the HfO2 and the Ta-containing thin films indicate that the processes that lead to the attenuation of growth are associated mostly with the second half-cycle of ALD (H2O or NH3 exposure). The length of the incubation time is found to correlate with both the total enthalpy change of the overall ALD reaction, as well as the net internal energy change of a single ligand exchange reaction representative of the second half of the ALD reaction. These results suggest that the reaction thermochemistry, and activation barriers for the reactions involved the ALD process play a key role in determining the length of the incubation period caused by PEI.
Characterization of Mo/Si multilayer growth on stepped topographies
Authors: van den Boogaard A. J. R. , Louis E. , Zoethout E. , Goldberg K. A. , Bijkerk F.
Published: September 2011

Mo/Si multilayer mirrors with nanoscale bilayer thicknesses have been deposited on stepped substrate topographies, using various deposition angles. The multilayer morphology at the step-edge region was studied by cross section transmission electron microscopy. A transition from a continuous- to columnar layer morphology is observed near the step-edge, as a function of the local angle of incidence of the deposition flux. Taking into account the corresponding kinetics and anisotropy in layer growth, a continuum model has been developed to give a detailed description of the height profiles of the individual continuous layers. Complementary optical characterization of the multilayer system using a microscope operating in the extreme ultraviolet wavelength range, revealed that the influence of the step-edge on the planar multilayer structure is restricted to a region within 300 nm from the step-edge.
Entrainment of a Population of Synthetic Genetic Oscillators
Authors: Mondragón-Palomino Octavio , Danino Tal , Selimkhanov Jangir , Tsimring Lev , Hasty Jeff
Published: September 2011

A positive-feedback loop in a biological oscillator allows effective setting of the clock by external cues.
Out of Tibet: Pliocene Woolly Rhino Suggests High-Plateau Origin of Ice Age Megaherbivores
Authors: Deng Tao , Wang Xiaoming , Fortelius Mikael , Li Qiang , Wang Yang , Tseng Zhijie J. , Takeuchi Gary T. , Saylor Joel E. , Säilä Laura K. , Xie Guangpu
Published: September 2011

The Tibetan Plateau acted as a cradle of adaptation to cold for Pleistocene megafauna.
The Overlooked Back End of the Nuclear Fuel Cycle
Authors: Macfarlane Allison M.
Published: September 2011

The recent accident at the Fukushima nuclear power plant reinforces the need for renewed thinking about nuclear-waste storage and disposal.
Epigenetic Licensing of Germline Gene Expression by Maternal RNA in
C. elegans
Authors: Johnson Cheryl L. , Spence Andrew M.
Published: September 2011

Expression of a gene in an offspring needs an RNA (but not the protein it codes for) provided by its mother.
That's Incredible!
The Believing Brain
From Ghosts and Gods to Politics and Conspiracies—How We Construct Beliefs and Reinforce Them as Truths

by Michael Shermer

Times Books (Henry Holt), New York, 2011. 400 pp. $28, C$32. ISBN 9780805091250.
Authors: Jost John T.
Published: September 2011

Seeing the brain as "a belief engine," Shermer discusses cognitive tools that lead us to "reinforce our beliefs as truths."
Canny Minds and Uncanny Questions
Man-Made Minds
Living with Thinking Machines

Faith Salie (moderator), Hod Lipson, David Ferrucci, Eric Horvitz, and Rodney Brooks

A panel discussion. World Science Festival, New York. 4 June 2011.
Authors: Wayne Greg , Pasternack Alex
Published: September 2011

A panel at this year's World Science Festival discussed the current state, future prospects, and potential impacts of "thinking machines."
Synthetic Biology: Regulating Industry Uses of New Biotechnologies
Authors: Erickson Brent , Singh Rina , Winters Paul
Published: September 2011

In our view, synthetic biology is an extension of the continuum of genetic science that has been used safely for more than 40 years by the biotechnology industry in the development of commercial products. Examples of synthetic biology use by biotechnology companies illustrate the potential to substantially reduce research and development time and to increase speed to market. Improvements in the speed and cost of DNA synthesis are enabling scientists to design modified bacterial chromosomes that can be used in the production of renewable chemicals, biofuels, bioproducts, renewable specialty chemicals, pharmaceutical intermediates, fine chemicals, food ingredients, and health care products. Regulatory options should support innovation and commercial development of new products while protecting the public from potential harms.
Demystifying DNA Demethylation
Authors: Nabel Christopher S. , Kohli Rahul M.
Published: September 2011

DNA modifying and repair enzymes make a new connection in the mechanism of DNA demethylation.
Understanding the Enemy
Authors: Velculescu Victor E. , Diaz Luis A.
Published: September 2011

A genomics approach shortens the path to discovery of a diagnostic gene fusion for a specific vascular cancer.
Dexamethasone-Induced Cytokine Changes Associated with Diminished Disease Severity in Horses Infected with Anaplasma phagocytophilum
Authors: Davies R. S. , Madigan J. E. , Hodzic E. , Borjesson D. L , Dumler J. S.
Published: September 2011

Anaplasma phagocytophilum
is the zoonotic cause of granulocytic anaplasmosis. We hypothesized that immune response, specifically gamma interferon (IFN-γ), plays a role in disease severity. To test this, horses were infected and
IFNG
expression was pharmacologically downregulated using corticosteroids. Eight horses were infected with
A. phagocytophilum
; 4 received dexamethasone on days 4 to 8 of infection. Clinical signs, hematologic parameters, and transcription of cytokine/chemokine genes were compared among treated and untreated horses. Infection was quantitated by
msp2
real-time PCR and microscopy. As anticipated, there was significantly greater leukopenia, thrombocytopenia, and anemia in infected versus uninfected horses. The
A. phagocytophilum
load was higher for dexamethasone-treated horses. Dexamethasone reduced
IFNG
transcription by day 12 and
IL-8
and
IL-18
by days 7 to 9 and increased
IL-4
on day 7. The ratio of
IL-10
to
IFNG
was increased by dexamethasone on day 9. There were no hematologic differences between the infected horses. Dexamethasone suppression of proinflammatory response resulted in delayed infection-induced limb edema and decreased icterus, anorexia, and reluctance to move between days 6 and 9 and lower fever on day 7. These results underscore the utility of the equine model of granulocytic anaplasmosis and suggest that Th1 proinflammatory response plays a role in worsening disease severity and that disease severity can be decreased by modulating proinflammatory response. A role for Th1 response and macrophage activation in hematologic derangements elicited by
A. phagocytophilum
is not supported by these data and remains unproven.
Intranasal Administration of an Inactivated Yersinia pestis Vaccine with Interleukin-12 Generates Protective Immunity against Pneumonic Plague
Authors: Kumar Devender , Kirimanjeswara Girish , Metzger Dennis W.
Published: September 2011

Inhalation of
Yersinia pestis
causes pneumonic plague, which rapidly progresses to death. A previously licensed killed whole-cell vaccine is presently unavailable due to its reactogenicity and inconclusive evidence of efficacy. The present study now shows that vaccination intranasally (i.n.) with inactivated
Y. pestis
CO92 (iYp) adjuvanted with interleukin-12 (IL-12) followed by an i.n. challenge with a lethal dose of
Y. pestis
CO92 prevented bacterial colonization and protected 100% of mice from pneumonic plague. Survival of the vaccinated mice correlated with levels of systemic and lung antibodies, reduced pulmonary pathology and proinflammatory cytokines, and the presence of lung lymphoid cell aggregates. Protection against pneumonic plague was partially dependent upon Fc receptors and could be transferred to naïve mice with immune mouse serum. On the other hand, protection was not dependent upon complement, and following vaccination, depletion of CD4 and/or CD8 T cells before challenge did not affect survival. In summary, the results demonstrate the safety, immunogenicity, and protective efficacy of i.n. administered iYp plus IL-12 in a mouse model of pneumonic plague.
Age-Specific Seroprevalence of Merkel Cell Polyomavirus, BK Virus, and JC Virus
Authors: Viscidi Raphael P. , Rollison Dana E. , Sondak Vernon K. , Silver Barbara , Messina Jane L. , Giuliano Anna R. , Fulp William , Ajidahun Abidemi , Rivanera Daniela
Published: September 2011

We produced capsids of Merkel cell polyomavirus (MCPyV) in a baculovirus expression system and developed a virus-like particle (VLP) enzyme-linked immunosorbent assay (ELISA). To determine age-specific seroprevalence, serum samples were collected from 947 individuals attending hospital outpatient clinics and ranging in age from 1 to 93 years. To evaluate the association between exposure to MCPyV and Merkel cell cancer (MCC), plasma samples were obtained from 33 MCC patients and 37 controls. MCPyV seroprevalence was 45% in children under 10 years of age, increased to 60% in the next decade of life, and peaked at 81% among those 60 to 69 years of age. Levels of MCPyV capsid antibodies were positively correlated with age (P= 0.007). Virus specificity of MCPyV seroreactivity was supported by competitive inhibition of reactivity by MCPyV VLPs and not by BK polyomavirus (BKPyV) VLPs. MCPyV seroprevalence was greater among MCC patients (91%) than controls (68%; age-adjustedPvalue, 0.32); the mean level of MCPyV antibodies was also greater (P= 0.04). The age-specific seroprevalence of MCPyV shares with previously known polyomaviruses, BKPyV and JC polyomavirus (JCPyV), evidence of widespread exposure in human populations beginning early in life. MCPyV age-specific seroprevalence also has unique features. Seroprevalence among children is higher than that of JCPyV but lower than that of BKPyV. Among older adults, MCPyV seroprevalence remains high, while that of BKPyV declines and that of JCPyV continues to rise. In agreement with results from other studies, we found an association between MCPyV seropositivity and MCC, and higher levels of serum MCPyV capsid antibodies in MCC patients than in controls.
Multilocus Sequence Typing of Streptococcus pneumoniae by Use of Mass Spectrometry
Authors: Dunne Eileen M. , Ong Eng Kok , Moser Ralf J. , Siba Peter M. , Phuanukoonnon Suparat , Greenhill Andrew R. , Robins-Browne Roy M. , Mulholland E. Kim , Satzke Catherine
Published: September 2011

Multilocus sequence typing (MLST) is an important tool for the global surveillance of bacterial pathogens that is performed by comparing the sequences of designated housekeeping genes. We developed and tested a novel mass spectrometry-based method for MLST of
Streptococcus pneumoniae
. PCR amplicons were subjected to
in vitro
transcription and base-specific cleavage, followed by analysis of the resultant fragments by using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). Comparison of the cleavage fragment peak patterns to a reference sequence set permitted automated identification of alleles. Validation experiments using 29 isolates of
S. pneumoniae
revealed that the results of MALDI-TOF MS MLST matched those obtained by traditional sequence-based MLST for 99% of alleles and that the MALDI-TOF MS method accurately identified two single-nucleotide variations. The MADLI-TOF MS method was then used for MLST analysis of 43
S. pneumoniae
isolates from Papua New Guinean children. The majority of the isolates present in this population were not clonal and contained seven new alleles and 30 previously unreported sequence types.
Genetic Response to Bacteriophage Infection in Lactococcus lactis Reveals a Four-Strand Approach Involving Induction of Membrane Stress Proteins,
d
-Alanylation of the Cell Wall, Maintenance of Proton Motive Force, and Energy Conservation
Authors: Fallico Vincenzo , Ross R. Paul , Fitzgerald Gerald F. , McAuliffe Olivia
Published: September 2011

In this study, whole-genome microarrays were used to gain insights into the global molecular response of
Lactococcus lactis
subsp.
lactis
IL1403 at an early stage of infection with the lytic phage c2. The bacterium differentially regulated the expression of 61 genes belonging to 14 functional categories, including cell envelope processes (12 genes), regulatory functions (11 genes), and carbohydrate metabolism (7 genes). The nature of these genes suggests a complex response involving four main mechanisms: (i) induction of membrane stress proteins, (ii)
d
-alanylation of cell wall lipoteichoic acids (LTAs), (iii) maintenance of the proton motive force (PMF), and (iv) energy conservation. The phage presence is sensed as a membrane stress in
L. lactis
subsp.
lactis
IL1403, which activated a cell wall-targeted response probably orchestrated by the concerted action of membrane phage shock protein C-like homologues, the global regulator SpxB, and the two-component system CesSR. The bacterium upregulated genes (
ddl
and
dltABCD
) responsible for incorporation of
d
-alanine esters into LTAs, an event associated with increased resistance to phage attack in Gram-positive bacteria. The expression of genes (
yshC
,
citE
,
citF
) affecting both PMF components was also regulated to restore the physiological PMF, which was disrupted following phage infection. While mobilizing the response to the phage-mediated stress, the bacterium activated an energy-saving program by repressing growth-related functions and switching to anaerobic respiration, probably to sustain the PMF and the overall cell response to phage. To our knowledge, this represents the first detailed description in
L. lactis
of the molecular mechanisms involved in the host response to the membrane perturbations mediated by phage infection.
Mechanism of Glycyrrhizic Acid Inhibition of Kaposi's Sarcoma-Associated Herpesvirus: Disruption of CTCF-Cohesin-Mediated RNA Polymerase II Pausing and Sister Chromatid Cohesion
Authors: Kang Hyojeung , Lieberman Paul M.
Published: September 2011

Glycyrrhizic acid (GA), a derivative of licorice, selectively inhibits the growth of lymphocytes latently infected with Kaposi's sarcoma-associated herpesvirus. The mechanism involves the deregulation of the multicistronic latency transcript, including the failure to generate the mature forms of viral mRNA encoding LANA. We show here that GA disrupts an RNA polymerase II (RNAPII) complex that accumulates at the CTCF-cohesin binding site within the first intron of the latency transcript. GA altered the enrichment of the RNAPII pausing complex, along with pausing factors SPT5 and NELF-A, at the intragenic CTCF-cohesin binding sites. GA blocked the interaction of cohesin subunit SMC3 with another cohesin subunit, RAD21, and reduced SPT5 interaction with RNAPII. Covalent coupling of GA to a solid support revealed that GA interacts with several cellular proteins, including SMC3 and SPT5, but not their respective interaction partners RAD21 and RNAPII. GA treatment also inhibited the transcription of some cellular genes, like c-
myc
, which contain a similar CTCF-cohesin binding site within the first intron. We also found that GA leads to a more general loss of sister chromatid cohesion for cellular chromosomes. These findings suggest that RNAPII pauses at intragenic CTCF-cohesin binding sites and that abrogation of this pausing by GA leads to loss of proper mRNA production and defects in sister chromatid cohesion, a process important for both viral and cellular chromosome stability.
Identification of Autographa californica Nucleopolyhedrovirus ac93 as a Core Gene and Its Requirement for Intranuclear Microvesicle Formation and Nuclear Egress of Nucleocapsids
Authors: Yuan Meijin , Huang Zhenqiu , Wei Denghui , Hu Zhaoyang , Yang Kai , Pang Yi
Published: September 2011

Autographa californica
nucleopolyhedrovirus (AcMNPV)
orf93
(
ac93
) is a highly conserved uncharacterized gene that is found in all of the sequenced baculovirus genomes except for
Culex nigripalpus
NPV. In this report, using bioinformatics analyses,
ac93
and
odv-e25
(
ac94
) were identified as baculovirus core genes and thus
p33-ac93-odv-e25
represent a cluster of core genes. To investigate the role of
ac93
in the baculovirus life cycle, an
ac93
knockout AcMNPV bacmid was constructed via homologous recombination in
Escherichia coli
. Fluorescence and light microscopy showed that the AcMNPV
ac93
knockout did not spread by infection, and titration assays confirmed a defect in budded virus (BV) production. However, deletion of
ac93
did not affect viral DNA replication. Electron microscopy indicated that
ac93
was required for the egress of nucleocapsids from the nucleus and the formation of intranuclear microvesicles, which are precursor structures of occlusion-derived virus (ODV) envelopes. Immunofluorescence analyses showed that Ac93 was concentrated toward the cytoplasmic membrane in the cytoplasm and in the nuclear ring zone in the nucleus. Western blot analyses showed that Ac93 was associated with both nucleocapsid and envelope fractions of BV, but only the nucleocapsid fraction of ODV. Our results suggest that
ac93
, although not previously recognized as a core gene, is one that plays an essential role in the formation of the ODV envelope and the egress of nucleocapsids from the nucleus.
Identification of Human Endogenous Retrovirus-Specific T Cell Responses in Vertically HIV-1-Infected Subjects
Authors: Tandon Ravi , SenGupta Devi , Ndhlovu Lishomwa C. , Vieira Raphaella G. S. , Jones R. Brad , York Vanessa A. , Vieira Vinicius A. , Sharp Elizabeth R. , Wiznia Andrew A. , Ostrowski Mario A. , Rosenberg Michael G. , Nixon Douglas F.
Published: September 2011

Human endogenous retrovirus (HERV)-specific T cell responses in HIV-1-infected adults have been reported. Whether HERV-specific immunity exists in vertically HIV-1-infected children is unknown. We performed a cross-sectional analysis of HERV-specific T cell responses in 42 vertically HIV-1-infected children. HERV (-H, -K, and -L family)-specific T cell responses were identified in 26 of 42 subjects, with the greatest magnitude observed for the responses to HERV-L. These HERV-specific T cell responses were inversely correlated with the HIV-1 plasma viral load and positively correlated with CD4
+
T cell counts. These data indicate that HERV-specific T cells may participate in controlling HIV-1 replication and that certain highly conserved HERV-derived proteins may serve as promising therapeutic vaccine targets in HIV-1-infected children.
Coxsackievirus A24 Variant Uses Sialic Acid-Containing
O
-Linked Glycoconjugates as Cellular Receptors on Human Ocular Cells
Authors: Mistry Nitesh , Inoue Hirotoshi , Jamshidi Fariba , Storm Rickard J. , Oberste M. Steven , Arnberg Niklas
Published: September 2011

Coxsackievirus A24 variant (CVA24v) is a main causative agent of acute hemorrhagic conjunctivitis (AHC), which is a highly contagious eye infection. Previously it has been suggested that CVA24v uses sialic acid-containing glycoconjugates as attachment receptors on corneal cells, but the nature of these receptors is poorly described. Here, we set out to characterize and identify the cellular components serving as receptors for CVA24v. Binding and infection experiments using corneal cells treated with deglycosylating enzymes or metabolic inhibitors of
de novo
glycosylation suggested that the receptor(s) used by CVA24v are constituted by sialylated
O
-linked glycans that are linked to one or more cell surface proteins but not to lipids. CVA24v bound better to mouse L929 cells overexpressing human P-selectin glycoprotein ligand-1 (PSGL-1) than to mock-transfected cells, suggesting that PSGL-1 is a candidate receptor for CVA24v. Finally, binding competition experiments using a library of mono- and oligosaccharides mimicking known PSGL-1 glycans suggested that CVA24v binds to Neu5Acα2,3Gal disaccharides (Neu5Ac is
N
-acetylneuraminic acid). These results provide further insights into the early steps of the CVA24v life cycle.
A Physical Link between the Pseudorabies Virus Capsid and the Nuclear Egress Complex
Authors: Leelawong Mindy , Guo Dongsheng , Smith Gregory A.
Published: September 2011

Following their assembly, herpesvirus capsids exit the nucleus by budding at the inner nuclear membrane. Two highly conserved viral proteins are required for this process, pUL31 and pUL34. In this report, we demonstrate that the pUL31 component of the pseudorabies virus nuclear egress complex is a conditional capsid-binding protein that is unmasked in the absence of pUL34. The interaction between pUL31 and capsids was confirmed through fluorescence microscopy and Western blot analysis of purified intranuclear capsids. Three viral proteins were tested for their abilities to mediate the pUL31-capsid interaction: the minor capsid protein pUL25, the portal protein pUL6, and the terminase subunit pUL33. Despite the requirement for each protein in nuclear egress, none of these viral proteins were required for the pUL31-capsid interaction. These findings provide the first formal evidence that a herpesvirus nuclear egress complex interacts with capsids and have implications for how DNA-containing capsids are selectively targeted for nuclear egress.
Role of the Two Sialic Acid Binding Sites on the Newcastle Disease Virus HN Protein in Triggering the Interaction with the F Protein Required for the Promotion of Fusion
Authors: Mahon Paul J. , Mirza Anne M. , Iorio Ronald M.
Published: September 2011

Newcastle disease virus (NDV)-induced membrane fusion requires an interaction between the hemagglutinin-neuraminidase (HN) attachment and the fusion (F) proteins, triggered by HN′s binding to receptors. NDV HN has two sialic acid binding sites: site I, which also mediates neuraminidase activity, and site II, which straddles the membrane-distal end of the dimer interface. By characterizing the effect on receptor binding avidity and F-interactive capability of HN dimer interface mutations, we present evidence consistent with (i) receptor engagement by site I triggering the interaction with F and (ii) site II functioning to maintain high-avidity receptor binding during the fusion process.
The Encapsidated Genome of Microplitis demolitor Bracovirus Integrates into the Host Pseudoplusia includens
Authors: Beck Markus H. , Zhang Shu , Bitra Kavita , Burke Gaelen R. , Strand Michael R.
Published: September 2011

Polydnaviruses (PDVs) are symbionts of parasitoid wasps that function as gene delivery vehicles in the insects (hosts) that the wasps parasitize. PDVs persist in wasps as integrated proviruses but are packaged as circularized and segmented double-stranded DNAs into the virions that wasps inject into hosts. In contrast, little is known about how PDV genomic DNAs persist in host cells.
Microplitis demolitor
carries
Microplitis demolitor
bracovirus (MdBV) and parasitizes the host
Pseudoplusia includens
. MdBV infects primarily host hemocytes and also infects a hemocyte-derived cell line from
P. includens
called CiE1 cells. Here we report that all 15 genomic segments of the MdBV encapsidated genome exhibited long-term persistence in CiE1 cells. Most MdBV genes expressed in hemocytes were persistently expressed in CiE1 cells, including members of the
glc
gene family whose products transformed CiE1 cells into a suspension culture. PCR-based integration assays combined with cloning and sequencing of host-virus junctions confirmed that genomic segments J and C persisted in CiE1 cells by integration. These genomic DNAs also rapidly integrated into parasitized
P. includens
. Sequence analysis of wasp-viral junction clones showed that the integration of proviral segments in
M. demolitor
was associated with a wasp excision/integration motif (WIM) known from other bracoviruses. However, integration into host cells occurred in association with a previously unknown domain that we named the host integration motif (HIM). The presence of HIMs in most MdBV genomic DNAs suggests that the integration of each genomic segment into host cells occurs through a shared mechanism.
The M Segment of the 2009 New Pandemic H1N1 Influenza Virus Is Critical for Its High Transmission Efficiency in the Guinea Pig Model
Authors: Chou Yi-ying , Albrecht Randy A. , Pica Natalie , Lowen Anice C. , Richt Jürgen A. , García-Sastre Adolfo , Palese Peter , Hai Rong
Published: September 2011

A remarkable feature of the 2009 pandemic H1N1 influenza virus is its efficient transmissibility in humans compared to that of precursor strains from the triple-reassortant swine influenza virus lineage, which cause only sporadic infections in humans. The viral components essential for this phenotype have not been fully elucidated. In this study, we aimed to determine the viral factors critical for aerosol transmission of the 2009 pandemic virus. Single or multiple segment reassortments were made between the pandemic A/California/04/09 (H1N1) (Cal/09) virus and another H1N1 strain, A/Puerto Rico/8/34 (H1N1) (PR8). These viruses were then tested in the guinea pig model to understand which segment of Cal/09 virus conferred transmissibility to the poorly transmissible PR8 virus. We confirmed our findings by generating recombinant A/swine/Texas/1998 (H3N2) (sw/Tx/98) virus, a representative triple-reassortant swine virus, containing segments of the Cal/09 virus. The data showed that the M segment of the Cal/09 virus promoted aerosol transmissibility to recombinant viruses with PR8 and sw/Tx/98 virus backgrounds, suggesting that the M segment is a critical factor supporting the transmission of the 2009 pandemic virus.
A Conserved Peptide in West Nile Virus NS4A Protein Contributes to Proteolytic Processing and Is Essential for Replication
Authors: Ambrose R. L. , Mackenzie J. M.
Published: September 2011

The West Nile virus strain Kunjin virus (WNV
KUN
) NS4A protein is a multifunctional protein involved in membrane proliferation, stimulation of cellular pathways, and evasion of host defense and is a major component of the WNV
KUN
RNA replication complex. We identified a highly conserved region (
120
P-E-P-E
123
) upstream of the viral protease dibasic cleavage site and investigated whether this motif was required for WNV
KUN
replication. Single point mutations to alanine and a PEPE deletion mutation were created in a full-length infectious WNV
KUN
molecular clone. All mutations drastically impaired viral replication and virion production, except that of the P122A mutant, which was slightly attenuated. These mutations were subsequently transferred to a WNV
KUN
replicon to specifically assess effects on RNA replication alone. Again, all mutants, except P122A, showed severely reduced negative-sense RNA production as well as decreased viral protein production. Correspondingly, immunofluorescence analyses showed a lack of double-stranded RNA (dsRNA) labeling and a dispersed localization of the WNV
KUN
proteins, suggesting that replication complex formation was additionally impaired. Attempts to rescue replication via conservative mutants largely failed except for substitution of Asp at E121, suggesting that a negative charge at this residue is equally important. Analysis of viral protein processing suggested that cleavage of the 2K peptide from NS4A did not occur with the mutant constructs. These observations imply that the combined effects of proline and negatively charged residues within the PEPE peptide are essential to promote the cleavage of 2K from NS4A, which is a prerequisite for efficient WNV replication.
Molecular Mechanism of Scanning and Start Codon Selection in Eukaryotes
Authors: Hinnebusch Alan G.
Published: September 2011

The correct translation of mRNA depends critically on the ability to initiate at the right AUG codon. For most mRNAs in eukaryotic cells, this is accomplished by the scanning mechanism, wherein the small (40S) ribosomal subunit attaches to the 5′ end of the mRNA and then inspects the leader base by base for an AUG in a suitable context, using complementarity with the anticodon of methionyl initiator tRNA (Met-tRNA
i
Met
) as the key means of identifying AUG. Over the past decade, a combination of yeast genetics, biochemical analysis in reconstituted systems, and structural biology has enabled great progress in deciphering the mechanism of ribosomal scanning. A robust molecular model now exists, describing the roles of initiation factors, notably eukaryotic initiation factor 1 (eIF1) and eIF1A, in stabilizing an “open” conformation of the 40S subunit with Met-tRNA
i
Met
bound in a low-affinity state conducive to scanning and in triggering rearrangement into a “closed” conformation incompatible with scanning, which features Met-tRNA
i
Met
more tightly bound to the “P” site and base paired with AUG. It has also emerged that multiple DEAD-box RNA helicases participate in producing a single-stranded “landing pad” for the 40S subunit and in removing the secondary structure to enable the mRNA to traverse the 40S mRNA-binding channel in the single-stranded form for base-by-base inspection in the P site.
Numerical simulation of an instrumented cantilever retaining wall
Authors: Chugh Ashok K. , Labuz Joseph F.
Published: September 2011

The field data of an instrumented cantilever retaining wall are reexamined to develop a working hypothesis for the mechanism that explains the observed response. The field data are in terms of earth pressures and wall movements (deflection, translation, and rotation) from the start to completion of backfilling. The observed response demonstrates strong interaction between the retaining wall and foundation soil. Traditional calculations based on earth pressure coefficients had not provided a satisfactory explanation for the measured responses during placement of backfill. In this paper, the working hypothesis, and results from its implementation in a continuum-mechanics-based computer program are presented. The numerical model results, displacements and earth pressures, are in general agreement with the field data for all stages of backfill placement and provide a clear exposition to the observed response. Practical implications of the work are included.