bluuebunny/crossref_metadata_2025_split huggingface dataset:
TheSalmonella entericaSerotype Typhi Vi Capsular Antigen Is Expressed after the Bacterium Enters the Ileal Mucosa
Authors: Tran Quynh T. , Gomez Gabriel , Khare Sangeeta , Lawhon Sara D. , Raffatellu Manuela , Bäumler Andreas J. , Ajithdoss Dharani , Dhavala Soma , Adams L. Garry 
Published: November 2009

ABSTRACTSalmonella entericaserotype Typhi, the etiological agent of typhoid fever, produces the Vi capsular antigen, a virulence factor absent inSalmonella entericaserotype Typhimurium. Previous studies suggest that the capsule-encodingviaBlocus reduces inflammatory responses in intestinal tissue; however, there are currently no data regarding the in vivo expression of this locus. Here we implemented direct and indirect methods to localize and detect Vi antigen expression within polarized intestinal epithelial cells and in the bovine ileal mucosa. We report thattviB, a gene necessary for Vi production inS.Typhi, was significantly upregulated during invasion of intestinal epithelial cells in vitro. During infection of bovine ligated loops,tviBwas expressed at levels significantly higher in calf tissue than those in the inoculum. The presence of the Vi capsular antigen was detected in calf ileal tissue via fluorescence microscopy. Together, these results support the concept that expression of the Vi capsular antigen is induced whenS.Typhi transits from the intestinal lumen into the ileal mucosa.
Some aspects of the mechanics of arching in backfilled stopes
Authors: Fahey Martin , Helinski Matthew , Fourie Andy 
Published: November 2009

In current underground mining using “open stoping” methods, it is common to backfill mined-out voids (“stopes”) using hydraulically placed backfill, which is commonly composed of tailings, to which cement is often added. Knowledge of the stress state within a backfilled stope is required for safe design of drawpoint barricades and for other operational reasons. This stress state depends, inter alia, on the degree of “arching” that occurs, resulting from the development of shear stress between the fill and the stope walls. This paper presents a numerical modelling study of aspects of the arching phenomenon, carried using the computer code Plaxis. The backfill is characterized using the Mohr–Coulomb soil model, and both dry backfill and saturated backfill are considered to completely cover the full spectrum of backfill types that are used in practice. It is shown that even with dry backfill, the behaviour is governed by a complex interaction between the soil parameters. The behaviour is more complex with saturated backfill, with a key parameter being the permeability of the backfill relative to the rate of filling — i.e., whether the backfilling operation can be considered to be “drained” or “undrained” or somewhere between these two extremes.
Interpretation of cone penetration tests — a unified approach
Authors: Robertson P. K. 
Published: November 2009

The electric cone penetration test (CPT) has been in use for over 40 years and is growing in popularity in North America. This paper provides some recent updates on the interpretation of some key geotechnical parameters in an effort to develop a more unified approach. Extensive use is made of the normalized soil behaviour type (SBTn) chart based on normalized cone resistance (Qt) and normalized friction ratio (Fr). Updates are provided regarding the normalization process and its application to the identification of soil type. The seismic CPT has provided extensive data linking CPT net cone resistance to shear-wave velocity and soil modulus. New correlations are presented in the form of contours of key parameters on the SBTn chart. These new relationships enable a more unified interpretation of CPT results over a wide range of soils. Updates are also provided in terms of in situ state parameter, peak friction angle, and soil sensitivity. The correlations are evaluated using available laboratory and full-scale field test results. Many of the recommendations contained in this paper are focused on low to moderate risk projects where empirical interpretation tends to dominate. For projects where more advanced methods are more appropriate, the recommendations provided in this paper can be used as a screening to evaluate critical regions–zones where selective additional in situ testing and sampling maybe appropriate.
Response of a polyvinyl chloride water pipe when transverse to an underlying pipe replaced by pipe bursting
Authors: Cholewa J. A. , Brachman R. W.I. , Moore I. D. 
Published: November 2009

An existing deteriorated or hydraulically undersized pipe can be replaced with a new pipe by static pipe bursting. Cavity expansion during pipe bursting induces ground movements, which may potentially damage nearby buried utilities if they are in close proximity to the pipe bursting operation. A large-scale pipe bursting experiment was performed in an 8 m long, 8 m wide, and 3 m deep test pit filled with a well-graded sand and gravel soil. A polyvinyl chloride (PVC) pipe, crossing transversely and 0.45 m above the existing pipe being replaced, was instrumented with strain gages to quantify the response of that transverse utility to the ground movements associated with pipe bursting. In this paper, the measured strain and corresponding deflection of the PVC pipe are examined and compared with measurements of surface uplift. The maximum longitudinal strain measured in the pipe was less than 0.1% and its vertical diameter decreased by only 0.5%, suggesting that ground displacements induced by pipe bursting did not jeopardize the transverse water pipe’s long-term performance, provided its joints were not damaged. A simplified design equation is introduced and shown to provide estimates of maximum longitudinal strain in the PVC pipe close to those measured during the laboratory experiment.
Sheddase Activity of Tumor Necrosis Factor-α Converting Enzyme Is Increased and Prognostically Valuable in Head and Neck Cancer
Authors: Ge Lisheng , Baskic Dejan , Basse Per , Vujanovic Lazar , Unlu Sebnem , Yoneyama Toshie , Vujanovic Andrea , Han Jie , Bankovic Dragic , Szczepanski Miroslaw J. , Hunt Jennifer L. , Herberman Ronald B. , Gollin Susanne M. , Ferris Robert L. , Whiteside Theresa L. , Myers Eugene N. , Vujanovic Nikola L. 
Published: November 2009

Abstract
Tumor necrosis factor α converting enzyme (TACE) is a sheddase overexpressed in cancers that generates cancer cell growth and survival factors, and is implicated in carcinogenesis and tumor growth. This indicates that TACE could be a potentially important cancer biomarker. Unexpectedly, TACE expression in cancer tissues does not correlate with cancer stage or invasiveness. Although TACE sheddase activity is a more direct and potentially better indicator of TACE biology and might be a better cancer biomarker than TACE expression, it has not been studied in cancer tissues. In the present study, we developed a reliable specific assay for quantification of TACE sheddase activity, investigated TACE activity and TACE protein expression in head and neck cancer (HNC) tissues, and examined the correlation of the results with HNC clinical stages and likelihood to recur. We found that HNC cell lines and tissues contained remarkably higher quantities of TACE activity and TACE protein than normal keratinocytes or oral mucosa. siRNA silencing of TACE resulted in the inhibition of release of the tumorogenic factors amphiregulin and transforming growth factor α, and tumor protective factors tumor necrosis factor receptors from HNC cells. Importantly, TACE activity, but not TACE protein expression, was significantly higher in large, T3/T4, primary tumors relative to small, T1/T2, primary tumors, and especially in primary tumors likely to recur relative to those unlikely to recur. These data show that increased TACE activity in cancer is biologically and clinically relevant, and indicate that TACE activity could be a significant biomarker of cancer prognosis. (Cancer Epidemiol Biomarkers Prev 2009;18(11):2913–22)
Association between Lifestyle Factors and CpG Island Methylation in a Cancer-Free Population
Authors: Brait Mariana , Ford Jean G. , Papaiahgari Srinivas , Garza Mary A. , Lee Jin I. , Loyo Myriam , Maldonado Leonel , Begum Shahnaz , McCaffrey Lee , Howerton Mollie , Sidransky David , Emerson Mark R. , Ahmed Saifuddin , Williams Carla D. , Hoque Mohammad Obaidul 
Published: November 2009

Abstract
Background: Many risk factors have been associated with cancer, such as age, family history, race, smoking, high-fat diet, and poor nutrition. It is important to reveal the molecular changes related to risk factors that could facilitate early detection, prevention, and overall control of cancer.
Methods: We selected six cancer-specific methylated genes that have previously been reported in primary tumors and have also been detected in different bodily fluids of cancer patients. Here, we used quantitative fluorogenic real-time methylation-specific PCR in plasma DNA samples for the detection of methylation changes from an asymptomatic population who do not have any known cancer.
Results: The promoter methylation frequencies of the studied genes were as follows: APC (7%), CCND2 (22%), GSTP1 (2%), MGMT (9%), RARβ2 (29%), and P16 (3%). Promoter methylation of at least one of the genes analyzed was observed in ∼46% (72 of 157) of the samples by binary dichotomization. Promoter hypermethylation of at least two genes was detected in 17% (26 of 157) of the samples. RARβ2 methylation was observed in 45% of subjects who had a high-fat diet in contrast with those who had a low-fat diet (23%; P = 0.007).
Discussion: Our findings may help to elucidate early methylation changes that may lead to cancer development. These methylation changes could be due to exposure to risk factors and may be useful for cancer prevention measures such as changes in lifestyle. Longitudinal follow-up of a high-risk population is needed to understand the association of methylation of candidate genes in cancer development. (Cancer Epidemiol Biomarkers Prev 2009;18(11):2984–91)
Human Papillomavirus 16 Load and E2/E6 Ratio in HPV16-Positive Women: Biomarkers for Cervical Intraepithelial Neoplasia ≥2 in a Liquid-Based Cytology Setting?
Authors: Boulet Gaëlle A.V. , Benoy Ina H. , Depuydt Christophe E. , Horvath Caroline A.J. , Aerts Marc , Hens Niel , Vereecken Annie J. , Bogers Johannes J. 
Published: November 2009

Abstract
This retrospective case-control study assessed human papillomavirus 16 (HPV16) viral load and E2/E6 ratio as risk markers for cervical intraepithelial neoplasia (CIN) ≥2 lesions in HPV16-positive women in a routine liquid-based cytology setting. Triplex quantitative PCR for HPV16 E6, E2, and β-globin was done to determine the HPV16 load and the E2/E6 ratio, as a surrogate marker for integration, for women with a negative histologic endpoint (200 controls: 83 normal histology and 117 CIN1) and women with a ≥CIN2 endpoint (180 cases: 41 CIN2, 122 CIN3, and 17 invasive carcinoma). Our analysis showed a significantly higher HPV16 load in the case group, which was completely attributable to the high viral load of samples with invasive carcinoma as histologic endpoint. There was no significant difference in viral load between the other histologic groups. The E2/E6 ratio proved to be lower for the cases. However, the E2/E6 ratio indicated the presence of HPV integration in a considerable amount of control samples (44.3%), which suggests that HPV integration occurs early in the development of cancer and undermines the clinical value of viral integration. Overall, the intrinsic heterogeneous nature of the cervical cytology samples caused a substantial overlap of the HPV16 load and the E2/E6 ratio between controls and cases, which precludes the determination of cutoff values for risk prediction and hampers the clinical applicability in a cervical screening setting. (Cancer Epidemiol Biomarkers Prev 2009;18(11):2992–9)
Associations between Silicone Skin Cast Score, Cumulative Sun Exposure, and Other Factors in the Ausimmune Study: A Multicenter Australian Study
Authors: Lucas Robyn M. , Ponsonby Anne-Louise , Dear Keith , Taylor Bruce V. , Dwyer Terence , McMichael Anthony J. , Valery Patricia , van der Mei Ingrid , Williams David , Pender Michael P. , Chapman Caron , Coulthard Alan , Kilpatrick Trevor 
Published: November 2009

AbstractPast sun exposure is linked to a wide range of disease outcomes but is difficult to measure accurately. Silicone skin casts measure skin damage, but some studies show that age rather than sun exposure is the most important determinant of cast score. We examined skin damage scores from silicone casts of the back of the hand in a large adult sample (n = 534) with a broad range of past cumulative UV radiation (UVR) doses. Participants were ages 18 to 61 years and resided in one of four locations down the eastern Australian seaboard, spanning 27-43°S. Data were collected by questionnaire and during a nurse-led interview and examination. Silicone casts were graded from 1 to 6, where higher score represents greater damage. Higher skin damage score was associated with lighter skin pigmentation [adjusted odds ratio (AOR), 4.51; 95% confidence interval (95% CI), 2.33-8.75], fairer natural hair color, particularly red hair (AOR, 11.31; 95% CI, 4.08-31.36), and blue/gray eyes (AOR, 1.72; 95% CI, 1.14-2.59). Higher cumulative UVR dose, particularly before age 18 years, was associated with higher skin damage score (AOR, 2.06; 95% CI, 1.15-2.67 per 1,000 KJ/m2), as was number of sunburns, even after adjustment for cumulative UVR dose (AOR, 2.86; 95% CI, 1.50-5.43 for &gt;10 sunburns ever compared with no sunburns ever). Silicone casts of the dorsum of the hand provide a measure of cumulative UVR dose and number of sunburns over the lifetime, which persists after adjustment for chronological age. They can be used as an objective measure of cumulative past sun exposure in epidemiologic studies, but other determinants of skin damage, such as skin pigmentation, should be concurrently evaluated. (Cancer Epidemiol Biomarkers Prev 2009;18(11):2887–94)
Genetic Variants of Methyl Metabolizing Enzymes and Epigenetic Regulators: Associations with Promoter CpG Island Hypermethylation in Colorectal Cancer
Authors: de Vogel Stefan , Wouters Kim A.D. , Gottschalk Ralph W.H. , van Schooten Frederik J. , de Goeij Anton F.P.M. , de Bruïne Adriaan P. , Goldbohm Royle A. , van den Brandt Piet A. , Weijenberg Matty P. , van Engeland Manon 
Published: November 2009

Abstract
Aberrant DNA methylation affects carcinogenesis of colorectal cancer. Folate metabolizing enzymes may influence the bioavailability of methyl groups, whereas DNA and histone methyltransferases are involved in epigenetic regulation of gene expression. We studied associations of genetic variants of folate metabolizing enzymes (MTHFR, MTR, and MTRR), DNA methyltransferase DNMT3b, and histone methyltransferases (EHMT1, EHMT2, and PRDM2), with colorectal cancers, with or without the CpG island methylator phenotype (CIMP), MLH1 hypermethylation, or microsatellite instability. Incidence rate ratios were calculated in case-cohort analyses, with common homozygotes as reference, among 659 cases and 1,736 subcohort members of the Netherlands Cohort Study on diet and cancer (n = 120,852). Men with the MTHFR 677TT genotype were at decreased colorectal cancer risk (incidence rate ratio, 0.49; P = 0.01), but the T allele was associated with increased risk in women (incidence rate ratio, 1.39; P = 0.02). The MTR 2756GG genotype was associated with increased colorectal cancer risk (incidence rate ratio, 1.58; P = 0.04), and inverse associations were observed among women carrying DNMT3b C→T (rs406193; incidence rate ratio, 0.72; P = 0.04) or EHMT2 G→A (rs535586; incidence rate ratio, 0.76; P = 0.05) polymorphisms. Although significantly correlated (P &lt; 0.001), only 41.5% and 33.3% of CIMP tumors harbored MLH1 hypermethylation or microsatellite instability, respectively. We observed inverse associations between MTR A2756G and CIMP among men (incidence rate ratio, 0.58; P = 0.04), and between MTRR A66G and MLH1 hypermethylation among women (incidence rate ratio, 0.55; P = 0.02). In conclusion, MTHFR, MTR, DNMT3b, and EHMT2 polymorphisms are associated with colorectal cancer, and rare variants of MTR and MTRR may reduce promoter hypermethylation. The incomplete overlap between CIMP, MLH1 hypermethylation, and microsatellite instability indicates that these related “methylation phenotypes” may not be similar and should be investigated separately. (Cancer Epidemiol Biomarkers Prev 2009;18(11):3086–96)
Telomere Length in Peripheral Leukocyte DNA and Gastric Cancer Risk
Authors: Hou Lifang , Savage Sharon A. , Blaser Martin J. , Perez-Perez Guillermo , Hoxha Mirjam , Dioni Laura , Pegoraro Valeria , Dong Linda M. , Zatonski Witold , Lissowska Jolanta , Chow Wong-Ho , Baccarelli Andrea 
Published: November 2009

Abstract
Telomere length reflects lifetime cumulative oxidative stress from environmental exposures, such as cigarette smoking and chronic inflammation. Shortened telomere length is thought to cause genomic instability and has been associated with several cancers. We examined the association of telomere length in peripheral leukocyte DNA with gastric cancer risk as well as potential confounding factors and risk modifiers for telomere length–related risk. In a population-based study of gastric cancer conducted in a high-risk population in Warsaw, Poland, between 1994 and 1996, we measured relative telomere length in 300 cases and 416 age- and gender-matched controls using quantitative real-time PCR. Among controls, telomeres were significantly shorter in association with aging (P &lt; 0.001), increasing pack-years of cigarette smoking (P = 0.02), decreasing fruit intake (P = 0.04), and Helicobacter pylori positivity (P = 0.03). Gastric cancer cases had significantly shorter telomere length (mean ± SD relative telomere length, 1.25 ± 0.34) than controls (1.34 ± 0.35; P = 0.0008). Gastric cancer risk doubled [odds ratio (OR), 2.04; 95% confidence interval (95% CI), 1.33-3.13] among subjects in the shortest compared with the highest quartile of telomere length (Ptrend &lt; 0.001). Telomere length–associated risks were higher among individuals with the lowest risk profile, those H. pylori–negative (OR, 5.45; 95% CI, 2.10-14.1), nonsmokers (OR, 3.07; 95% CI, 1.71-5.51), and individuals with high intake of fruits (OR, 2.43; 95% CI, 1.46-4.05) or vegetables (OR, 2.39; 95% CI, 1.51-3.81). Our results suggest that telomere length in peripheral leukocyte DNA was associated with H. pylori positivity, cigarette smoking, and dietary fruit intake. Shortened telomeres increased gastric cancer risk in this high-risk Polish population. (Cancer Epidemiol Biomarkers Prev 2009;18(11):3103–9)
A Local Area Analysis of Racial, Ethnic, and Neighborhood Disparities in Breast Cancer Staging
Authors: Echeverría Sandra E. , Borrell Luisa N. , Brown Diane , Rhoads George 
Published: November 2009

Abstract
Few studies have examined the role of neighborhood socioeconomic condition in shaping breast cancer disparities in defined local areas. We tested associations between three measures of neighborhood socioeconomic condition (poverty, median income, and a composite neighborhood score) on breast cancer staging in two urban counties of the state of New Jersey. Data for these counties were obtained from the New Jersey Surveillance, Epidemiology, and End Results tumor registry and were selected because of their large racial/ethnic and socioeconomic diversity and pilot prevention efforts taking place in these areas. Our study population included Black, Latina, and White women (N = 4,589) diagnosed with breast cancer from 1999 to 2004. Each cancer case was geocoded and linked to socioeconomic data obtained from the 2000 U.S. census. Census tracts served as proxies for neighborhoods. Logistic regression models accounting for clustering of individuals within neighborhoods were fitted with Generalized Estimating Equations. Women living in neighborhoods with lower versus higher neighborhood scores were significantly more likely to have advanced-stage disease (odds ratio, 1.6; confidence intervals, 1.1-2.3), after adjusting for age at diagnosis and race/ethnicity. In analyses stratified by race/ethnicity, results remained significant for all neighborhood measures for White and Black women, but not for Latinas. Moreover, neighborhood poverty showed a weaker socioeconomic gradient in breast cancer staging among White women. Our study findings support the use of a multidimensional neighborhood index to better capture differences in cancer staging risk across racial/ethnic groups and provides evidence that population-based cancer data could be used to identify local needs specific to local populations. (Cancer Epidemiol Biomarkers Prev 2009;18(11):3024–9)
Sequence Variant on 3q28 and Urinary Bladder Cancer Risk: Findings from the Los Angeles-Shanghai Bladder Case-Control Study
Authors: Stern Mariana C. , Van Den Berg David , Yuan Jian-Min , Conti David V. , Gago-Dominguez Manuela , Pike Malcolm C. , Xiang Yong-Bing , Gao Yu-Tang , Cortessis Victoria K. 
Published: November 2009

Abstract
Recently, the first genome-wide association study of bladder cancer identified an association of genome-wide significance between single nucleotide polymorphism (SNP) rs715021 and urinary bladder cancer risk among European individuals. This SNP is in a haplotype block in linkage disequilibrium with the TP63 gene. We investigated the role of this SNP among 1,042 cases and 1,123 controls among non-Latino whites in Los Angeles County, CA and among Chinese in Shanghai, China. We confirmed an association between the A allele and bladder cancer risk [log-additive per A allele odds ratios (OR), 1.24; and 95% confidence intervals (95% CI), 1.02-1.52; P = 0.032] in Los Angeles County and a similar association in Shanghai (log-additive per A allele OR, 1.21; 95% CI, 0.98-1.49; P = 0.080). These estimates did not differ by study site, smoking status, or gender. However, the effects were greater in older individuals. Analysis within non-Latino whites, for whom we had histologic results, revealed that this association was restricted to low-risk tumors (OR, 1.49; 95% CI, 1.17-1.92; P = 0.002) and absent among high-risk tumors (OR, 1.03; 95% CI, 0.80-1.33; P = 0.790; heterogeneity, P = 0.019). A positive association (OR, 1.56; 95% CI, 0.93-2.62; P = 0.089) was only observed among high-risk tumors from individuals older than 56 years old (interaction, P = 0.045). Our results suggest that a TP63 gene variant may increase susceptibility for the development of urinary bladder tumors with low risk of progression. (Cancer Epidemiol Biomarkers Prev 2009;18(11):3057–61)