bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantitative PCR for detection and discrimination of the bloodborne pathogen Staphylococcus epidermidis in platelet preparations using divIVA and icaA as target genes
Authors: Mastronardi Cherie Cameron , Ramírez-Arcos Sandra 
Published: November 2007

Bacterial contamination of blood components is the major microbiological cause of transfusion-associated morbidity, with Staphylococcus epidermidis being the most frequently isolated organism from contaminated platelet preparations (PPs). We have recently shown that S. epidermidis forms biofilms during platelet storage, which might account for reported missed detection during routine screening. In this study, we developed a highly sensitive and specific multiplex quantitative PCR (QPCR) assay to detect S. epidermidis in PPs at levels of 102–103 cfu/mL. A specific primer pair and hydrolysis probe were designed to amplify an internal region of the cell division divIVA gene that is unique to S. epidermidis. In addition, an internal sequence of the virulence gene icaA, which is involved in the synthesis of the S. epidermidis biofilm matrix, was selected to allow for differentiation of potentially biofilm-forming S. epidermidis isolates. A conserved region of the 8 alleles of the HLA-DQα1 locus present in residual white blood cells in PPs was selected as an internal control for the assay. The specificity of this assay was confirmed, as other staphylococcal species that were tested with the optimized parameters were not detected. This QPCR assay could be adaptable for the detection of other bloodborne bacterial pathogens.
Fluoroquinolone resistance ofSerratia marcescens: sucrose, salicylate, temperature, and pH induction of phenotypic resistance
Authors: Begic Sanela , Worobec Elizabeth A. 
Published: November 2007

Serratia marcescens is a nosocomial agent with a natural resistance to a broad spectrum of antibiotics, making the treatment of its infections very challenging. This study examines the influence of salicylate, sucrose, temperature, and pH variability on membrane permeability and susceptibility of S. marcescens to norfloxacin (hydrophilic fluoroquinolone) and nalidixic acid (hydrophobic quinolone). Resistance of wild-type S. marcescens UOC-67 (ATCC 13880) to norfloxacin and nalidixic acid was assessed by minimal inhibitory concentration (MIC) assays after growth in the presence of various concentrations of sucrose and salicylate and different temperatures and pH values. Norfloxacin and nalidixic acid accumulation was determined in the absence and presence of (i) carbonyl cyanide m-chlorophenylhydrazone (CCCP), a proton-motive-force collapser, and (ii) Phe-Arg β-naphthylamide (PAβN), an efflux pump inhibitor. Accumulation of norfloxacin decreased when S. marcescens was grown in high concentrations of salicylate (8 mmol/L) and sucrose (10% m/v), at high temperature (42 °C), and at pH 6, and it was restored in the presence of CCCP because of the collapse of proton-gradient-dependent efflux in S. marcescens. Although nalidixic acid accumulation was observed, it was not affected by salicylate, sucrose, pH, or temperature changes. In the absence of PAβN, and either in the presence or absence of CCCP, a plateau was reached in the nalidixic acid accumulation for all environmental conditions. With the addition of 20 mg/L PAβN nalidixic acid accumulation is restored for all environmental conditions, suggesting that this quinolone is recognized by a yet to be identified S. marcescens pump that does not use proton motive force as its energy source.
EDP auditing in the 1980's or the vanishing paper trail
Authors: Andersen Richard E. 
Published: November 2007

This paper is designed to provide an overview of (1) traditional auditing methodology and (2) the reasons why these methods must be modified and adapted in order to cope with the "vanishing paper trail" inherent in today's (and tomorrow's) increasingly on-line, data base-oriented, distributed processing, EDP environment.
The three basic types off audits (general, administrative, and applications) will be discussed. Examples of flagrant, and not-so-flagrant, computer crimes will be presented. Practical and proposed solutions for the reduction of these types of DP crimes in the 1980's will be examined.
The major thrust of the paper, however, will address the importance of the applications-oriented audit. The paper will discuss the concept of Computer Management Technology (CMT), and show that this is in reality a type of on-going auditing task. Alternatives will be examined for measuring, managing and controlling key functional areas that have a definite interactive effect on the availability of resources and the performance of system components (or both) in a data processing installation.
Galanin Is Up-Regulated in Colon Adenocarcinoma
Authors: Kim Kye Young , Kee Mee K. , Chong Seon Ah , Nam Myeong Jin 
Published: November 2007

Abstract
The early diagnosis of colorectal cancer and the early detection of recurrence are central to effective treatment, as prognosis is directly related to the stage of the disease. When colorectal cancer is diagnosed at an early, localized stage, 5-year survival is 90%. There is substantial interest in the identification of circulating human tumor-derived proteins in serum for the purposes of early cancer diagnosis. We have implemented an approach based on the analysis of microarray data for the identification of tumor proteins that may have utility as biomarkers in colon cancer. Expression analysis of microarray data obtained from a variety of 290 tumors and normal tissues revealed that galanin was maximally expressed in colon cancer. These findings were corroborated by real-time quantitative PCR, in which the colon cancer cell lines LOVO, HCT15, SW480, and SW620 cell showed significantly higher levels of galanin expression than did noncolon cancer cell lines. To evaluate galanin as a potential biomarker of colon cancer, a preliminary “training” set of serum from 40 healthy donors and 55 colon cancer patients was analyzed by ELISA. The data pattern was confirmed by an independent set of 90 masked serum samples: 24 from healthy donors and 66 from colon cancer patients. This result yielded a sensitivity of 69.7% [95% confidence interval (95% CI), 57.1-80.4], specificity of 75.0% (95% CI, 53.3-90.2), and positive predictive value of 88.5% (95% CI, 76.6-95.7). The galanin expression level was significantly increased with tumor size and tumor stage. These findings justify a prospective assessment of serum galanin protein as a screening tool for colon cancer. (Cancer Epidemiol Biomarkers Prev 2007;16(11):2373–8)
Assessment of the Relation between Biomarkers for Smoking and Biomarkers for Acrylamide Exposure in Humans
Authors: Vesper Hubert W. , Bernert John T. , Ospina Maria , Meyers Tunde , Ingham Leigha , Smith Antoinette , Myers Gary L. 
Published: November 2007

Abstract
Smoking is an important source of acrylamide exposure in the general population. We assessed the relationship between hemoglobin adducts of acrylamide (HbAA) and glycidamide (HbGA) as biomarkers of acrylamide exposure and plasma cotinine (PC) as biomarkers of tobacco smoke exposure in 94 men and 67 women. The median (5th-95th percentile) biomarker concentrations (pmol/g Hb) in the group of individuals with PC concentrations of ≤10 ng/mL were 51 (29-155) and 34 (16-117) for HbAA and HbGA, respectively. They were significantly lower than those in the group of individuals with PC concentrations of &gt;10 ng/mL [194 (87-403) and 107 (41-215) for HbAA and HbGA, respectively]. In individuals with PC concentrations of &lt;1 ng/mL, HbAA and HbGA were similar to those observed in the group with PC values of ≤10 ng/mL. The intersubject variability was profoundly smaller in the group with PC values of ≤10 ng/mL compared with the group with PC values of &gt;10 ng/mL. Although HbAA and HbGA could be categorized into distinguishable groups using PC concentration ranges commonly used to categorize presumed smokers and nonsmokers, no significant relationship was observed between these two biomarkers and PC within each group. The different exposure periods reflected by these biomarkers and the resulting different susceptibility to short-term variations in exposure patterns may in part explain these observations. The findings suggest that tobacco smoke exposure in individuals with PC values of &lt;1 ng/mL has only a minimal effect on HbAA and HbGA. (Cancer Epidemiol Biomarkers Prev 2007;16(11):2471–8)
Bronchial Epithelial Ki-67 Index Is Related to Histology, Smoking, and Gender, but Not Lung Cancer or Chronic Obstructive Pulmonary Disease
Authors: Miller York E. , Blatchford Patrick , Hyun Dae Sung , Keith Robert L. , Kennedy Timothy C. , Wolf Holly , Byers Tim , Bunn Paul A. , Lewis Marina T. , Franklin Wilbur A. , Hirsch Fred R. , Kittelson John 
Published: November 2007

Abstract
Purpose: To determine whether increased bronchial epithelial proliferation is associated with histology, smoking status, gender, age, chronic obstructive pulmonary disease (COPD), or lung cancer.
Experimental Design: Cross-sectional study of 113 subjects undergoing white light and autofluorescence bronchoscopy: 27 never smokers; 27 current or ex-smokers with normal spirometry; 31 current or ex-smokers with COPD; and 28 current, ex-, or never smokers with lung cancer. Ki-67 expresssion was determined by immunohistochemistry on all evaluable biopsy sites without carcinoma. Relationships between Ki-67 index (percentage of epithelial cells expressing Ki-67), demographic variables, smoking, histology, and the presence of COPD and/or lung cancer were determined.
Results: Results for both maximal and mean Ki-67 index are similar, so only the former are reported. Average maximal Ki-67 index was higher in current smokers than either ex-smokers or never smokers (48.0% versus 30.6% versus 22.6%; P &lt; 0.001). Males had higher Ki-67 index than females (39.9% versus 23.6%; P &lt; 0.001). Compared with subjects without disease (Ki-67 index = 30.0%), maximal Ki-67 index was not significantly elevated (P = 0.44) in subjects with either lung cancer (Ki-67 = 39.1%) or COPD (Ki-67 = 38.9%).
Conclusions: Smoking status, bronchial histology, and gender were significantly associated with Ki-67 index. No increase in Ki-67 index was found in the nonmalignant epithelium of patients with lung cancer or COPD. Although Ki-67 index may provide insight into the short-term effects of chemoprevention agents on cell proliferation, its lack of association with lung cancer or COPD raises question regarding its utility as a lung cancer risk biomarker. (Cancer Epidemiol Biomarkers Prev 2007;16(11):2425–31)
The Association of Gastric Cancer Risk with Plasma Folate, Cobalamin, and Methylenetetrahydrofolate Reductase Polymorphisms in the European Prospective Investigation into Cancer and Nutrition
Authors: Vollset Stein Emil , Igland Jannicke , Jenab Mazda , Fredriksen Åse , Meyer Klaus , Eussen Simone , Gjessing Håkon K. , Ueland Per Magne , Pera Guillem , Sala Núria , Agudo Antonio , Capella Gabriel , Del Giudice Giuseppe , Palli Domenico , Boeing Heiner , Weikert Cornelia , Bueno-de-Mesquita H. Bas , Carneiro Fátima , Pala Valeria , Vineis Paolo , Tumino Rosario , Panico Salvatore , Berglund Göran , Manjer Jonas , Stenling Roger , Hallmans Göran , Martínez Carmen , Dorronsoro Miren , Barricarte Aurelio , Navarro Carmen , Quirós José R. , Allen Naomi , Key Timothy J. , Bingham Sheila , Linseisen Jakob , Kaaks Rudolf , Overvad Kim , Tjønneland Anne , Büchner Frederike L. , Peeters Petra H.M. , Numans Mattijs E. , Clavel-Chapelon Françoise , Boutron-Ruault Marie-Christine , Trichopoulou Antonia , Lund Eiliv , Slimani Nadia , Ferrari Pietro , Riboli Elio , González Carlos A. 
Published: November 2007

Abstract
Previous studies have shown inconsistent associations of folate intake and polymorphisms of the methylenetetrahydrofolate reductase (MTHFR) gene with gastric cancer risk. Our nested case-control study within the European Prospective Investigation into Cancer and Nutrition cohort is the first prospective study of blood folate levels and gastric cancer. Gastric cancer cases (n = 247) and controls (n = 631) were matched for study center, age, sex, and time of blood donation. Two common single nucleotide polymorphisms of the MTHFR gene were determined, as were plasma concentrations of folate, cobalamin (vitamin B12), total homocysteine, and methylmalonic acid (cobalamin deficiency marker) in prediagnostic plasma. Risk measures were calculated with conditional logistic regression. Although no relations were observed between plasma folate or total homocysteine concentrations and gastric cancer, we observed a trend toward lower risk of gastric cancer with increasing cobalamin concentrations (odds ratio, 0.79 per SD increase in cobalamin; P = 0.01). Further analyses showed that the inverse association between cobalamin and gastric cancer was confined to cancer cases with low pepsinogen A levels (marker of severe chronic atrophic gastritis) at the time of blood sampling. The 677 C→T MTHFR polymorphism was not associated with gastric cancer, but we observed an increased risk with the variant genotype of the 1298 A→C polymorphism (odds ratio, 1.47 for CC versus AA; P = 0.04). In conclusion, we found no evidence of a role of folate in gastric cancer etiology. However, we observed increased gastric cancer risk at low cobalamin levels that was most likely due to compromised cobalamin status in atrophic gastritis preceding gastric cancer. (Cancer Epidemiol Biomarkers Prev 2007;16(11):2416–24)
Oral Contraceptive Use and Risk of Breast Carcinoma In situ
Authors: Nichols Hazel B. , Trentham-Dietz Amy , Egan Kathleen M. , Titus-Ernstoff Linda , Hampton John M. , Newcomb Polly A. 
Published: November 2007

Abstract
There is some indication that oral contraceptive use may be associated with a small increase in risk of invasive breast cancer; however, oral contraceptive use in relation to breast carcinoma in situ (BCIS) has rarely been studied. We investigated oral contraceptive use in relation to risk of BCIS in a large population-based case-control study. Female residents of Wisconsin, Massachusetts, and New Hampshire aged 20 to 74 years with a new diagnosis of BCIS (n = 1,878) were identified from statewide tumor registries in 1997 to 2001. Age-matched female controls (n = 8,041) were randomly selected from population lists. Information on oral contraceptive use and other risk factors was collected during structured telephone interviews. Odds ratios (OR) and 95% confidence intervals (95% CI) were estimated using logistic regression. In multivariate models, ever use of oral contraceptives was associated with a small and marginally significant increase in BCIS overall (OR, 1.11; 95% CI, 0.99-1.25) and for ductal carcinoma in situ (OR, 1.15; 95% CI, 1.01-1.31). No strong associations were detected according to age started, duration, time since first or last use, or oral contraceptive use relative to the first full-term pregnancy. The slightly increased risk of BCIS seemed limited to former users (OR, 1.13; 95% CI, 1.00-1.27) and women without a family history of breast cancer (OR, 1.16; 95% CI, 1.01-1.32 for ever versus never use). Consistent with invasive breast cancer, these results suggest that oral contraceptive use is at most a minor contributor to BCIS risk. (Cancer Epidemiol Biomarkers Prev 2007;16(11):2262–9)
Prostate Cancer Risk and ESR1 TA, ESR2 CA Repeat Polymorphisms
Authors: McIntyre Matthew H. , Kantoff Philip W. , Stampfer Meir J. , Mucci Lorelei A. , Parslow Diane , Li Haojie , Gaziano J. Michael , Abe Miyako , Ma Jing 
Published: November 2007

Abstract
Background: Experimental evidence has suggested that estrogen receptor α (coded by the gene ESR1) might increase prostate cancer risk, whereas estrogen receptor β (coded by the gene ESR2) might reduce prostate cancer risk.
Methods: We investigated the relationship with prostate cancer risk of both a TA repeat polymorphism in the ESR1 5′ region, ESR1 (TA)n, and with a CA repeat polymorphism in intron 5 of ESR2, ESR2 (CA)n, in a case-control study (545 cases and 674 controls) nested in the Physicians' Health Study.
Results: Prostate cancer risk was highest for carriers of ESR1 (TA)24 and ESR1 (TA)25. Replacing one modal ESR1 (TA)14 allele with one ESR1 (TA)24 allele yielded an odds ratio of 1.42 (95% confidence interval, 1.00-2.00; P = 0.05). Replacing one ESR1 (TA)14 allele with one ESR1 (TA)25 allele yielded an odds ratio of 2.10 (95% confidence interval, 1.15-3.84; P = 0.02). ESR2 (CA)n showed no effects on prostate cancer risk.
Conclusions: The ESR1 (TA)n polymorphism might play a role in prostate cancer risk. (Cancer Epidemiol Biomarkers Prev 2007;16(11):2233–6)
Frequency of Defective DNA Mismatch Repair in Colorectal Cancer among the Alaska Native People
Authors: Boardman Lisa A. , Lanier Anne P. , French Amy J. , Schowalter Karen V. , Burgart Lawrence J. , Koller Kathryn R. , McDonnell Shannon K. , Schaid Daniel J. , Thibodeau Stephen N. 
Published: November 2007

Abstract
The frequency of colorectal cancer (CRC) among the Alaska Native people is the highest of any ethnic group in the United States. In this study, CRC from 329 Alaska Native people (165 Eskimo, 111 Indians, and 53 Aleut) were evaluated for evidence of defective DNA mismatch repair (MMR) by testing tumors for altered protein expression (hMLH1, hMSH2, and hMSH6) and for the presence of microsatellite instability. Of the 329 samples tested, 46 (14%) showed both microsatellite instability and altered protein expression; 42 (91%) with a loss of hMLH1, 3 (7%) hMSH2, and 1 (2%) hMLH1/hMSH6. Tumors with loss of hMLH1 were further evaluated for hMLH1 promoter hypermethylation and for the presence of the BRAF-V600E mutation. Among cases tested, all 19 (100%) tumors among the Eskimo patients showed hMLH1 promoter hypermethylation, whereas this was the case for only 3 of the 7 (42%) tumors among the Aleut (P = 0.002) and 5 of the 10 (50%) tumors from the Indians (P = 0.002). The majority of hypermethylated cases (23 of 27) tested positive for the V600E alteration. Of the nine tumors from the Aleut and Indian patients that did not exhibit hMLH1 hypermethylation, eight tested negative for V600E. Overall, the frequency of defective MMR among the three groups was not statistically different (P = 0.75). However, the data suggest that the pathogenesis of CRC may differ between the three groups. The CRC with defective MMR among the Eskimo sample fit the typical profile for hMLH1-related cancer associated with sporadic CRC, whereas the pattern in the Aleut and Indian suggests the possibility that germ line hMLH1 mutations may be present. (Cancer Epidemiol Biomarkers Prev 2007;16(11):2344–50)
Ascorbate and Dehydroascorbic Acid as Reliable Biomarkers of Oxidative Stress: Analytical Reproducibility and Long-term Stability of Plasma Samples Subjected to Acidic Deproteinization
Authors: Lykkesfeldt Jens 
Published: November 2007

Abstract
Lack of post-sampling stability of ascorbate and dehydroascorbic acid and failure to block their in vivo equilibrium have lowered their value as biomarkers of oxidative stress and limited the ability to further investigate their possible role in disease prevention. In the present article, analytic reproducibility was tested by repeated analysis of plasma aliquots from one individual over 4 years. The plasma was subjected to acidic deproteinization with an equal volume of 10% meta-phosphoric acid containing 2 mmol/L of EDTA and analyzed for ascorbate and dehydroascorbic acid by high-performance liquid chromatography with coulometric detection. In a parallel experiment, the stability of human plasma samples treated as above and stored at −80°C for 5 years was tested in a cohort of 131 individuals. No degradation or shift in the equilibrium between ascorbate and dehydroascorbic acid was observed in either of the experiments. In conclusion, ascorbate and dehydroascorbic acid could be adequately preserved in plasma stored at −80°C following acidic deproteinization with meta-phosphoric acid containing 2 mmol/L of EDTA. (Cancer Epidemiol Biomarkers Prev 2007;16(11):2513–6)
Effects of Radar Beam Shielding on Rainfall Estimation for the Polarimetric C-Band Radar
Authors: Friedrich Katja , Germann Urs , Gourley Jonathan J. , Tabary Pierre 
Published: November 2007

Abstract
Radar reflectivity (Zh), differential reflectivity (Zdr), and specific differential phase (Kdp) measured from the operational, polarimetric weather radar located in Trappes, France, were used to examine the effects of radar beam shielding on rainfall estimation. The objective of this study is to investigate the degree of immunity of Kdp-based rainfall estimates to beam shielding for C-band radar data during four typical rain events encountered in Europe. The rain events include two cold frontal rainbands with average rainfall rates of 7 and 17 mm h−1, respectively, and two summertime convective rain events with average rainfall rates of 11 and 22 mm h−1.
The large effects of beam shielding on rainfall accumulation were observed for algorithms using Zh and Zdr with differences of up to ∼2 dB (40%) compared to a Kdp-based algorithm over a power loss range of 0–8 dB. This analysis reveals that Zdr and Kdp are not affected by partial beam shielding. Standard reflectivity corrections based on the degree of beam shielding would have overestimated rainfall rates by up to 1.5 dB for less than 40% beam shielding and up to 3 dB for beam shielding less than 75%. The investigation also examined the sensitivity of beam shielding effects on rainfall rate estimation to (i) axis–ratio parameterization and drop size distribution, (ii) methods used to smooth profiles of differential propagation phase (ϕdp) and estimate Kdp, and (iii) event-to-event variability. Although rainfall estimates were sensitive to drop size distribution and axis–ratio parameterization, differences between Zh- and Kdp-based rainfall rates increased independently from those parameters with amount of shielding. Different approaches to smoothing ϕdp profiles and estimating Kdp were examined and showed little impact on results.
In Situ Calibration of the SeaBird 9plus CTD Thermometer
Authors: Uchida Hiroshi , Ohyama Kentaro , Ozawa Satoshi , Fukasawa Masao 
Published: November 2007

Abstract
A Sea-Bird Electronics (SBE 35) deep ocean reference thermometer is used with the SBE 9plus CTD system to calibrate the SBE 3 ocean thermometers of the CTD. The SBE 35 is standardized in water-triple-point and gallium-melting-point cells. The SBE 3 is calibrated with the SBE 35 under the assumption that discrepancies between SBE 3 and SBE 35 data are due to pressure sensitivity, the viscous heating effect, and time drift of the SBE 3. Based on the results of an in situ calibration, the pressure sensitivity and the viscous heating effect were evaluated for 11 SBE 3 thermometers. Three SBE 3s showed little pressure sensitivity, and eight had pressure sensitivities of 1–2 mK at 6000 dbar. The average viscous heating effect on the standard SBE 3 measurements was 0.5 mK. Both the accuracy and precision of the in situ calibrated SBE 3 data at depths greater than 2000 dbar were 0.4 mK relative to the SBE 35 reference.