bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hepatitis C Virus Transmission Bottlenecks Analyzed by Deep Sequencing
Authors: Wang Gary P. , Sherrill-Mix Scott A. , Chang Kyong-Mi , Quince Chris , Bushman Frederic D. 
Published: April 2010

ABSTRACT
Hepatitis C virus (HCV) replication in infected patients produces large and diverse viral populations, which give rise to drug-resistant and immune escape variants. Here, we analyzed HCV populations during transmission and diversification in longitudinal and cross-sectional samples using 454/Roche pyrosequencing, in total analyzing 174,185 sequence reads. To sample diversity, four locations in the HCV genome were analyzed, ranging from high diversity (the envelope hypervariable region 1 [HVR1]) to almost no diversity (the 5′ untranslated region [UTR]). For three longitudinal samples for which early time points were available, we found that only 1 to 4 viral variants were present, suggesting that productive infection was initiated by a very small number of HCV particles. Sequence diversity accumulated subsequently, with the 5′ UTR showing almost no diversification while the envelope HVR1 showed >100 variants in some subjects. Calculation of the transmission probability for only a single variant, taking into account the measured population structure within patients, confirmed initial infection by one or a few viral particles. These findings provide the most detailed sequence-based analysis of HCV transmission bottlenecks to date. The analytical methods described here are broadly applicable to studies of viral diversity using deep sequencing.
Cell Entry of the Aphthovirus Equine Rhinitis A Virus Is Dependent on Endosome Acidification
Authors: Groppelli Elisabetta , Tuthill Tobias J. , Rowlands David J. 
Published: April 2010

ABSTRACT

Equine rhinitis A virus (ERAV) is genetically closely related to foot-and-mouth disease virus (FMDV), and both are now classified within the genus
Aphthovirus
of the family
Picornaviridae
. For disease security reasons, FMDV can be handled only in high-containment facilities, but these constraints do not apply to ERAV, making it an attractive alternative for the study of aphthovirus biology. Here, we show, using immunofluorescence, pharmacological agents, and dominant negative inhibitors, that ERAV entry occurs (as for FMDV) via clathrin-mediated endocytosis and acidification of early endosomes. This validates the use of ERAV as a model system to study the mechanism of cell entry by FMDV.
A Single Coxsackievirus B2 Capsid Residue Controls Cytolysis and Apoptosis in Rhabdomyosarcoma Cells
Authors: Gullberg Maria , Tolf Conny , Jonsson Nina , Polacek Charlotta , Precechtelova Jana , Badurova Miriam , Sojka Martin , Mohlin Camilla , Israelsson Stina , Johansson Kjell , Bopegamage Shubhada , Hafenstein Susan , Lindberg A. Michael 
Published: April 2010

ABSTRACT

Coxsackievirus B2 (CVB2), one of six human pathogens of the group B coxsackieviruses within the enterovirus genus of
Picornaviridae
, causes a wide spectrum of human diseases ranging from mild upper respiratory illnesses to myocarditis and meningitis. The CVB2 prototype strain Ohio-1 (CVB2O) was originally isolated from a patient with summer grippe in the 1950s. Later on, CVB2O was adapted to cytolytic replication in rhabdomyosarcoma (RD) cells. Here, we present analyses of the correlation between the adaptive mutations of this RD variant and the cytolytic infection in RD cells. Using reverse genetics, we identified a single amino acid change within the exposed region of the VP1 protein (glutamine to lysine at position 164) as the determinant for the acquired cytolytic trait. Moreover, this cytolytic virus induced apoptosis, including caspase activation and DNA degradation, in RD cells. These findings contribute to our understanding of the host cell adaptation process of CVB2O and provide a valuable tool for further studies of virus-host interactions.
Regulation of
De Novo
-Initiated RNA Synthesis in Hepatitis C Virus RNA-Dependent RNA Polymerase by Intermolecular Interactions
Authors: Chinnaswamy S. , Murali A. , Li P. , Fujisaki K. , Kao C. C. 
Published: April 2010

ABSTRACT

The hepatitis C virus (HCV) RNA-dependent RNA polymerase (RdRp) has been proposed to change conformations in association with RNA synthesis and to interact with cellular proteins.
In vitro
, the RdRp can initiate
de novo
from the ends of single-stranded RNA or extend a primed RNA template. The interactions between the Δ1 loop and thumb domain in NS5B are required for
de novo
initiation, although it is unclear whether these interactions are within an NS5B monomer or are part of a higher-order NS5B oligomeric complex. This work seeks to address how polymerase conformation and/or oligomerization affects
de novo
initiation. We have shown that an increasing enzyme concentration increases
de novo
initiation by the genotype 1b and 2a RdRps while primer extension reactions are not affected or inhibited under similar conditions. Initiation-defective mutants of the HCV polymerase can increase
de novo
initiation by the wild-type (WT) polymerase. GTP was also found to stimulate
de novo
initiation. Our results support a model in which the
de novo
initiation-competent conformation of the RdRp is stimulated by oligomeric contacts between individual subunits. Using electron microscopy and single-molecule reconstruction, we attempted to visualize the low-resolution conformations of a dimer of a
de novo
initiation-competent HCV RdRp.
Effect of Mutations in VP5* Hydrophobic Loops on Rotavirus Cell Entry
Authors: Kim Irene S. , Trask Shane D. , Babyonyshev Marina , Dormitzer Philip R. , Harrison Stephen C. 
Published: April 2010

ABSTRACT
Experiments in cell-free systems have demonstrated that the VP5* cleavage fragment of the rotavirus spike protein, VP4, undergoes a foldback rearrangement that translocates three clustered hydrophobic loops from one end of the molecule to the other. This conformational change resembles the foldback rearrangements of enveloped virus fusion proteins. By recoating rotavirus subviral particles with recombinant VP4 and VP7, we tested the effects on cell entry of substituting hydrophilic for hydrophobic residues in the clustered VP5* loops. Several of these mutations decreased the infectivity of recoated particles without preventing either recoating or folding back. In particular, the V391D mutant had a diminished capacity to interact with liposomes when triggered to fold back by serial protease digestion in solution, and particles recoated with this mutant VP4 were 10,000-fold less infectious than particles recoated with wild-type VP4. Particles with V391D mutant VP4 attached normally to cells and internalized efficiently, but they failed in the permeabilization step that allows coentry of the toxin α-sarcin. These findings indicate that the hydrophobicity of the VP5* apex is required for membrane disruption during rotavirus cell entry.
Either ZEB1 or ZEB2/SIP1 Can Play a Central Role in Regulating the Epstein-Barr Virus Latent-Lytic Switch in a Cell-Type-Specific Manner
Authors: Ellis Amy L. , Wang Zhenxun , Yu Xianming , Mertz Janet E. 
Published: April 2010

ABSTRACT

We previously reported that the cellular protein ZEB1 can repress expression of the Epstein-Barr virus (EBV)
BZLF1
gene in transient transfection assays by directly binding its promoter, Zp. We also reported that EBV containing a 2-bp substitution mutation in the ZEB-binding ZV element of Zp spontaneously reactivated out of latency into lytic replication at a higher frequency than did wild-type EBV. Here, using small interfering RNA (siRNA) and short hairpin RNA (shRNA) technologies, we definitively show that ZEB1 is, indeed, a key player in maintaining EBV latency in some epithelial and B-lymphocytic cell lines. However, in other EBV-positive epithelial and B-cell lines, another zinc finger E-box-binding protein, ZEB2/SIP1, is the key player. Both ZEB1 and ZEB2 can bind Zp via the ZV element. In EBV-positive cells containing only ZEB1, knockdown of ZEB1 led to viral reactivation out of latency, with synthesis of EBV immediate-early and early lytic gene products. However, in EBV-positive cells containing both ZEBs, ZEB2, not ZEB1, was the primary ZEB family member bound to Zp. Knockdown of ZEB2, but not ZEB1, led to EBV lytic reactivation. Thus, we conclude that either ZEB1 or ZEB2 can play a central role in the maintenance of EBV latency, doing so in a cell-type-dependent manner.
Effect of an electronic nicotine delivery device (e cigarette) on desire to smoke and withdrawal, user preferences and nicotine delivery: randomised cross-over trial
Authors: Bullen C , McRobbie H , Thornley S , Glover M , Lin R , Laugesen M 
Published: April 2010

ObjectivesTo measure the short-term effects of an electronic nicotine delivery device (“e cigarette”, ENDD) on desire to smoke, withdrawal symptoms, acceptability, pharmacokinetic properties and adverse effects.DesignSingle blind randomised repeated measures cross-over trial of the Ruyan V8 ENDD.SettingUniversity research centre in Auckland, New Zealand.Participants40 adult dependent smokers of 10 or more cigarettes per day.InterventionsParticipants were randomised to use ENDDs containing 16 mg nicotine or 0 mg capsules, Nicorette nicotine inhalator or their usual cigarette on each of four study days 3 days apart, with overnight smoking abstinence before use of each product.Main outcome measuresThe primary outcome was change in desire to smoke, measured as “area under the curve” on an 11-point visual analogue scale before and at intervals over 1 h of use. Secondary outcomes included withdrawal symptoms, acceptability and adverse events. In nine participants, serum nicotine levels were also measured.ResultsOver 60 min, participants using 16 mg ENDD recorded 0.82 units less desire to smoke than the placebo ENDD (p=0.006). No difference in desire to smoke was found between 16 mg ENDD and inhalator. ENDDs were more pleasant to use than inhalator (p=0.016) and produced less irritation of mouth and throat (p<0.001). On average, the ENDD increased serum nicotine to a peak of 1.3 mg/ml in 19.6 min, the inhalator to 2.1 ng/ml in 32 min and cigarettes to 13.4 ng/ml in 14.3 min.ConclusionsThe 16 mg Ruyan V8 ENDD alleviated desire to smoke after overnight abstinence, was well tolerated and had a pharmacokinetic profile more like the Nicorette inhalator than a tobacco cigarette. Evaluation of the ENDD for longer-term safety, potential for long-term use and efficacy as a cessation aid is needed.Trial registrationNo.12607000587404, Australia and New Zealand Clinical Trials Register
Human electroencephalography and the tobacco industry: a review of internal documents
Authors: Panzano Vincent C , Wayne Geoffrey Ferris , Pickworth Wallace B , Connolly Gregory N 
Published: April 2010

ObjectiveTo determine the extent and implications of internal human electroencephalography (EEG) research conducted by the tobacco industry.MethodsThis study analysed internal documents that describe the results of human EEG studies conducted by tobacco manufacturers. Emphasis was placed on documents that pertain to the application of EEG to product evaluation efforts.ResultsInternal EEG research was used to determine dose-response relations and effective threshold levels for nicotine, emphasising the importance of form and mechanism of nicotine delivery for initiating robust central nervous system (CNS) effects. Internal studies also highlight the importance of human behaviour during naturalistic smoking, revealing neurophysiological markers of compensation during smoking of reduced nicotine cigarettes. Finally, internal research demonstrates the effectiveness of EEG for the evaluation of non-nicotine phenomena including smoke-component discrimination by smokers, classification of sensory characteristics and measurement of hedonics and other subjective effects.ConclusionsTobacco manufacturers successfully developed objective, EEG-based techniques to evaluate the influence of product characteristics on acceptance and use. Internal results suggest that complex interactions between pharmacological, sensory and behavioural factors mediate the brain changes that occur with smoking. These findings have implications for current proposals regarding the regulation of tobacco products and argue for the incorporation of objective measures of product effects when evaluating the health risks of new and existing tobacco products.
Public support in England for a total ban on the sale of tobacco products
Authors: Shahab Lion , West Robert 
Published: April 2010

BackgroundThis study aimed to determine the level of support for a sales ban on tobacco in England to provide a benchmark against which any changes over time can be assessed.Methods8735 people from England who participated in one of five monthly cross-sectional household surveys in 2008 were asked to indicate whether they would support the statement that ‘the government should work towards banning the sale of tobacco completely within the next 10 years’. In addition, sociodemographic and smoking characteristics were assessed.ResultsA substantial proportion of the total sample (44.5%; 95% CI 43.5% to 45.6%) would support a move towards a complete ban. While never smokers (OR 2.02; 95% CI 1.82 to 2.25) and ex-smokers (OR 1.41; 95% CI 1.21 to 1.65) were more likely to support this idea, even among current smokers, a third would favour moving towards a sales ban of tobacco products. Adjusting for other background characteristics, younger, female participants, those living in London and those from lower socioeconomic groups were most likely to support a ban. Among smokers, a higher cigarette consumption, smoking enjoyment and contentment with being a smoker were associated with opposition to a ban, while feeling uncomfortable being a smoker, wanting to be a non-smoker and being worried about future health consequences of smoking were associated with support for a ban.ConclusionSupport for movement towards a ban on the sale of tobacco is higher than might be imagined. It is conceivable that as smoking prevalence falls further and smoking becomes more socially unacceptable, support might grow to a point where such a policy could become feasible.
Therapeutic Efficacy Evaluation of Curcumin on Human Oral Squamous Cell Carcinoma Xenograft Using Multimodalities of Molecular Imaging
Authors: Lin Yu-Chuan , Chen Hong-Wen , Kuo Yu-Cheng , Chang Ya-Fang , Lee Yi-Jang , Hwang Jeng-Jong 
Published: April 2010

Oral squamous cell carcinoma (OSCC) is the most common malignancy of the oral cavity; however the treatment approaches are still unsatisfactory. We used a luciferase-transfected animal model to evaluate the therapeutic effects of curcumin. Human oral squamous cell carcinoma SAS cell line was stably transfected with luc gene, named SAS/luc cells. For the in vivo study, they were inoculated subcutaneously to 6-week-old male NOD/SCID mice which were separated into four groups for intraperitoneal injection (i.p.) of curcumin: control, daily with 35 mg/kg, 70 mg/kg every 2 days, and 100 mg/kg every 3 days. We applied SAS/luc bearing animal model and bioluminescent imaging (BLI) to study the inhibition effect of curcumin on tumor growth. The cytotoxic effect of curcumin on SAS/luc cells was mainly at G2/M phase and a significant dose dependent increase of the apoptotic SAS/luc cells as represented by sub-G1 phase was shown. Therapeutic efficacy evaluated by both caliper assay and BLI showed a significant difference between curcumin-treated mice and the controls (p < 0.01). The significant inhibition effects of curcumin on the proliferation and the growth of human OSCC are observed both in vitro and in vivo. No significant body weight change (i.e. within 20%) was observed in all SAS/luc-bearing mice with or without curcumin treatment. This SAS/luc human OSCC bearing animal model combined with multimodalities of molecular imaging permits a sensitive and non-invasive approach to evaluate the therapeutic efficacy in vivo.
Manganese Superoxide Dismutase Polymorphism and Risk of Gastric Lesions, and Its Effects on Chemoprevention in a Chinese Population
Authors: Tu Hua-kang , Pan Kai-feng , Zhang Yang , Li Wen-qing , Zhang Lian , Ma Jun-ling , Li Ji-you , You Wei-cheng 
Published: April 2010

Abstract
Background: Manganese superoxide dismutase is the primary antioxidant enzyme in the mitochondria and is involved in carcinogenesis. To investigate the association between MnSOD Val16Ala polymorphism and risk of advanced gastric lesions, and its effects on chemoprevention, a population-based study was conducted in Linqu, a high-risk area of gastric cancer in China.
Methods: Genotypes were determined by PCR-RFLP analysis in 3,355 subjects with the baseline histopathologic diagnosis in 1994, and 2,758 of these subjects received subsequent three interventions including vitamin supplementation for 7.3 years. Odds ratios (OR) and 95% confidence intervals (CI) were estimated by unconditional logistic regression model.
Results: We found an increased risk of dysplasia in subjects with the Val/Ala+Ala/Ala genotype (OR, 1.31; 95% CI, 1.02-1.68) compared with the Val/Val genotype. Stratified analysis indicated that a significantly elevated risk of intestinal metaplasia (OR, 3.40; 95% CI, 2.64-4.38) or dysplasia (OR, 4.01; 95% CI, 2.79-5.74) was found in subjects carrying the Val/Ala+Ala/Ala genotype and Helicobacter pylori infection, and an interaction between this genotype and a high serum H. pylori IgG titer (&gt;2.94) on the risk of dysplasia was observed (Pinteraction = 0.01). Furthermore, an elevated chance for regression of gastric lesions was observed in subjects with the Val/Ala+Ala/Ala genotype and high IgG titer in an intervention trial with vitamin supplementation (OR, 2.45; 95% CI, 1.37-4.38).
Conclusions: These findings suggest that Val16Ala polymorphism may play an important role in development of advanced gastric lesions and modify the effect of vitamin supplementation on the evolution of gastric lesions.
Impact: Val16Ala polymorphism is related to gastric cancer development. Cancer Epidemiol Biomarkers Prev; 19(4); 1089–97. ©2010 AACR.
Comparison of Two Methods for Estimating Absolute Risk of Prostate Cancer Based on Single Nucleotide Polymorphisms and Family History
Authors: Hsu Fang-Chi , Sun Jielin , Zhu Yi , Kim Seong-Tae , Jin Tao , Zhang Zheng , Wiklund Fredrik , Kader A. Karim , Zheng S. Lilly , Isaacs William , Grönberg Henrik , Xu Jianfeng 
Published: April 2010

Abstract
Disease risk–associated single nucleotide polymorphisms (SNP) identified from genome-wide association studies have the potential to be used for disease risk prediction. An important feature of these risk-associated SNPs is their weak individual effect but stronger cumulative effect on disease risk. Several approaches are commonly used to model the combined effect in risk prediction, but their performance is unclear. We compared two methods to model the combined effect of 14 prostate cancer risk–associated SNPs and family history for the estimation of absolute risk for prostate cancer in a population-based case-control study in Sweden (2,899 cases and 1,722 controls). Method 1 weighs each risk allele equally using a simple method of counting the number of risk alleles, whereas method 2 weighs each risk SNP differently based on its odds ratio. We found considerable differences between the two methods. Absolute risk estimates from method 1 were generally higher than those of method 2, especially among men at higher risk. The difference in the overall discriminative performance, measured by area under the curve of the receiver operating characteristic, was small between method 1 (0.614) and method 2 (0.618), P = 0.20. However, the performance of these two methods in identifying high-risk individuals (2- or 3-fold higher than average risk), measured by positive predictive values, was higher for method 2 than for method 1. These results suggest that method 2 is superior to method 1 in estimating absolute risk if the purpose of risk prediction is to identify high-risk individuals. Cancer Epidemiol Biomarkers Prev; 19(4); 1083–8. ©2010 AACR.
Standards Affecting the Consistency of Gene Expression Arrays in Clinical Applications
Authors: Enkemann Steven A. 
Published: April 2010

AbstractThe use of microarray technology to measure gene expression has created optimism for the feasibility of using molecular assessments of tumors routinely in the clinical management of cancer. Gene expression arrays have been pioneers in the development of standards; both for research use and now for clinical application. Some of the existing standards have been driven by the early perception that microarray technology was inconsistent and perhaps unreliable. More recent experimentation has shown that reproducible data can be achieved and clinical standards are beginning to emerge. For the transcriptional assessment of tumors, this means a system that correctly samples a tumor, isolates RNA and processes this for microarray analysis, evaluates the data, and communicates findings in a consistent and timely fashion. The most important standard is to show that a clinically important assessment can be made with microarray data. The standards emerging from work on various parts of the entire process could guide the development of a workable system. However, the final standard for each component of the process depends on the accuracy required when the assay becomes part of the clinical routine: a routine that now includes the molecular evaluation of tumors. Cancer Epidemiol Biomarkers Prev; 19(4); 1000–3. ©2010 AACR.
Intra-Person Variation of Urinary Biomarkers of Oxidative Stress and Inflammation
Authors: Wu Xiaoyan , Cai Hui , Xiang Yong-Bing , Cai Qiuyin , Yang Gong , Liu Dake , Sanchez Stephanie , Zheng Wei , Milne Ginger , Shu Xiao-Ou 
Published: April 2010

Abstract
Background: Oxidative stress and inflammation have been linked to many chronic diseases including cancer and cardiovascular diseases. Urinary levels of F2-isoprostanes (F2-IsoPs), 2,3-dinor-5,6-dihydro-15-F2t-IsoP (15-F2t-IsoP-M), a major metabolite of F2-IsoPs, prostaglandin E2 metabolite (PGE-M), and leukotriene E4 (LTE4) have been proposed as biomarkers for oxidative stress and inflammation. However, little information is available regarding the intra-person variation of these biomarkers, hindering their application in epidemiologic studies.
Methods: We evaluated the intra-person variation of these four urinary biomarkers among 48 randomly chosen participants of a validation study of a population-based cohort, the Shanghai Men's Health Study. Four spot urine samples, collected during each season over a 1-year period, were measured for these biomarkers.
Results: The intraclass correlation coefficients for F2-IsoPs, 15-F2t-IsoP-M, PGE-M, and LTE4 were 0.69, 0.76, 0.67, and 0.64, respectively. The Spearman correlation coefficients, derived by using bootstrap analysis of single spot measurements and the average of the other three seasonal measurements, were 0.47, 0.60, 0.61, and 0.57 for F2-IsoPs, 15-F2t-IsoP-M, PGE-M, and LTE4. Except for high correlations between F2-IsoPs and 15-F2t-IsoP-M (r = 0.65), the other biomarkers were moderately correlated (r = 0.21-0.44).
Conclusions: Our study results suggest that these four urinary biomarkers have relatively low intra-person variation over a 1-year period.
Impact: Spot measurements of F2-IsoPs, 15-F2t-IsoP-M, PGE-M, and LTE4 could be useful as biomarkers of oxidative stress and inflammation status for epidemiologic studies. Cancer Epidemiol Biomarkers Prev; 19(4); 947–52. ©2010 AACR.