bluuebunny/crossref_metadata_2025_split huggingface dataset:
Determination of an Inoculum Effect with Various Cephalosporins among Clinical Isolates of Methicillin-Susceptible
Staphylococcus aureus
Authors: Nannini Esteban C. , Stryjewski Martin E. , Singh Kavindra V. , Rude Tom H. , Corey G. Ralph , Fowler Vance G. , Murray Barbara E. 
Published: March 2010

ABSTRACT

Using 98 clinical methicillin-susceptible
Staphylococcus aureus
isolates of known β-lactamase (Bla) type, we found a pronounced inoculum effect for cephalexin (mostly Bla type A and C strains), a mild inoculum effect for cephalothin (especially types B and C), and no inoculum effects for ceftriaxone and cefuroxime. Ceftobiprole showed the lowest MICs at a high inoculum but with a slight increase for Bla-positive versus Bla-negative strains. Since a potential therapeutic effect associated with a cephalosporin inoculum effect has been described, further studies are warranted.
Effect of NlpE Overproduction on Multidrug Resistance in
Escherichia coli
Authors: Nishino Kunihiko , Yamasaki Seiji , Hayashi-Nishino Mitsuko , Yamaguchi Akihito 
Published: March 2010

ABSTRACT

NlpE, an outer membrane lipoprotein, functions during envelope stress responses in Gram-negative bacteria. In this study, we report that overproduction of NlpE increases multidrug and copper resistance through activation of the genes encoding the AcrD and MdtABC multidrug efflux pumps in
Escherichia coli
.
Repair of Global Regulators inStaphylococcus aureus8325 and Comparative Analysis with Other Clinical Isolates
Authors: Herbert Silvia , Ziebandt Anne-Kathrin , Ohlsen Knut , Schäfer Tina , Hecker Michael , Albrecht Dirk , Novick Richard , Götz Friedrich 
Published: March 2010

ABSTRACTThe pathogenicity ofStaphylococcus aureusstrains varies tremendously (as seen with animals). It is largely dependent on global regulators, which control the production of toxins, virulence, and fitness factors. Despite the vast knowledge of staphylococcal molecular genetics, there is still widespread dispute over what factors must come together to make a strain highly virulent.S. aureusNCTC8325 (RN1 and derivatives) is a widely used model strain for which an incomparable wealth of knowledge has accumulated in the almost 50 years since its isolation. Although RN1 has functionalagr,sarA, andsaeglobal regulators, it is defective in two regulatory genes,rsbU(a positive activator of SigB) andtcaR(an activator of protein A transcription), and is therefore considered by many to be a poor model for studies of regulation and virulence. Here, we repaired these genes and compared the resulting RN1 derivatives with other widely used strains, Newman, USA300, UAMS-1, and COL, plus the parental RN1, with respect to growth, extracellular protein pattern, hemolytic activity, protein A production, pigmentation, biofilm formation, and mouse lethality. ThetcaR-repaired strain, showed little alteration in these properties. However, thersbU-repaired strain was profoundly altered. Hemolytic activity was largely decreased, the exoprotein pattern became much more similar to that of typical wild-type (wt)S. aureus, and there was a surprising increase in mouse lethality. We note that each of the strains tested has a mutational alteration in one or more other regulatory functions, and we conclude that the repaired RN1 is a good model strain for studies of staphylococcal regulation and pathobiology; although strain Newman has been used extensively for such studies in recent years, it has a missense mutation insaeS, the histidine kinase component of thesaesignaling module, which profoundly alters its regulatory phenotype. If this mutation were repaired, Newman would be considerably improved as a model strain.
CANDID
Authors: Bisht Prithvi , Madhusudan P. , Venkatakrishnan V. N. 
Published: March 2010

SQL injection attacks are one of the top-most threats for applications written for the Web. These attacks are launched through specially crafted user inputs, on Web applications that use low-level string operations to construct SQL queries. In this work, we exhibit a novel and powerful scheme for automatically transforming Web applications to render them safe against all SQL injection attacks.
A characteristic diagnostic feature of SQL injection attacks is that they change the intended structure of queries issued. Our technique for detecting SQL injection is to dynamically mine the programmer-intended query structure on any input, and detect attacks by comparing it against the structure of the actual query issued. We propose a simple and novel mechanism, called Candid, for mining programmer intended queries by dynamically evaluating runs over benign candidate inputs. This mechanism is theoretically well founded and is based on inferring intended queries by considering the symbolic query computed on a program run. Our approach has been implemented in a tool called Candid that retrofits Web applications written in Java to defend them against SQL injection attacks. We have also implemented Candid by modifying a Java Virtual Machine, which safeguards applications without requiring retrofitting. We report extensive experimental results that show that our approach performs remarkably well in practice.
Randomized Controlled Trial of a Psychosocial Telephone Counseling Intervention inBRCA1 andBRCA2 Mutation Carriers
Authors: Graves Kristi D. , Wenzel Lari , Schwartz Marc D. , Luta George , Wileyto Paul , Narod Steven , Peshkin Beth N. , Marcus Alfred , Cella David , Emsbo Susan Powell , Barnes Denise , Halbert Chanita Hughes 
Published: March 2010

AbstractBackground: Responses following BRCA1/2 genetic testing are relevant for the comprehension of risk status and may play a role in risk management decision making. The objective of this study was to evaluate a psychosocial telephone counseling (PTC) intervention delivered to BRCA1/2 mutation carriers following standard genetic counseling (SGC). We examined the effect of the intervention on distress and the concerns related to genetic testing.Methods: This prospective randomized clinical trial included 90 BRCA1/2 mutation carriers. We measured anxiety, depression, and genetic testing distress outcomes at intervention baseline and 6 and 12 months following disclosure. We evaluated the effects of SGC versus SGC plus PTC on psychological outcomes using intention-to-treat analyses through generalized estimating equations.Results: At 6 months, PTC reduced depressive symptoms (Z = −2.25, P = 0.02) and genetic testing distress (Z = 2.18, P = 0.02) compared with SGC. Furthermore, women in the intervention condition reported less clinically significant anxiety at 6 months (χ21 = 4.11, P = 0.04) than women who received SGC. We found no differences in outcomes between the intervention groups at the 12-month follow-up.Conclusions: As an adjunct to SGC, PTC delivered following disclosure of positive BRCA1/2 test results seems to offer modest short-term benefits for distress and anxiety. These results build upon a growing literature of psychosocial interventions for BRCA1/2 carriers and, given the potential impact of affect on risk management decision making, suggest that some carriers may derive benefits from adjuncts to traditional genetic counseling. Cancer Epidemiol Biomarkers Prev; 19(3); 648–54
Podoplanin and ABCG2: Malignant Transformation Risk Markers for Oral Lichen Planus
Authors: Shi Peng , Liu Wei , Zhou Zeng-Tong , He Qing-Bo , Jiang Wei-Wen 
Published: March 2010

Abstract
Background: Oral lichen planus (OLP) is a potentially malignant disorder associated with an increased risk for oral cancer. The purpose of this study was to determine protein expression of podoplanin and ATP-binding cassette, G2 subfamily (ABCG2) in patients with OLP and evaluate their use as biomarkers for OLP malignant transformation risk.
Methods: Podoplanin and ABCG2 expressions were determined in samples from 110 patients with untransformed OLP and 9 patients with malignant transformed OLP (mean follow-up of 5.1 years). We compared podoplanin expression, ABCG2 expression, and clinicopathologic parameters between the two groups.
Results: Podoplanin expression was observed in 48 of 110 (43.6%) cases of untransformed OLP and in 8 of 9 (88.9%) cases of transformed OLP. ABCG2 expression was found in 23 of 110 (20.9%) cases of untransformed OLP and in 6 of 9 (66.7%) cases of transformed OLP. Multivariate regression analysis revealed that podoplanin or ABCG2 expression was associated with 17.13-fold [95% confidence interval (95% CI), 1.71-171.22; P = 0.016] or 6.04-fold (95% CI, 1.20-30.36; P = 0.029) increased risk of malignant transformation, respectively. The risk of OLP malignant transformation was considerably higher with coexpression of podoplanin and ABCG2 than without coexpression of podoplanin and ABCG2 (odds ratio, 25.24; 95% CI, 4.48-142.27; P &lt; 0.001).
Conclusions: The expressions of podoplanin and ABCG2 in OLP were significantly associated with malignant transformation risk.
Impact: Our data suggested that podoplanin and ABCG2 may be used as biomarkers for risk assessment of oral malignant transformation in patients with OLP. Cancer Epidemiol Biomarkers Prev; 19(3); 844–9
Saliva-Derived DNA Performs Well in Large-Scale, High-Density Single-Nucleotide Polymorphism Microarray Studies
Authors: Bahlo Melanie , Stankovich Jim , Danoy Patrick , Hickey Peter F. , Taylor Bruce V. , Browning Sharon R. ,   The Australian and New Zealand Multiple Sclerosis Genetics Consortium (ANZgene), Brown Matthew A. , Rubio Justin P. 
Published: March 2010

Abstract
As of June 2009, 361 genome-wide association studies (GWAS) had been referenced by the HuGE database. GWAS require DNA from many thousands of individuals, relying on suitable DNA collections. We recently performed a multiple sclerosis (MS) GWAS where a substantial component of the cases (24%) had DNA derived from saliva. Genotyping was done on the Illumina genotyping platform using the Infinium Hap370CNV DUO microarray. Additionally, we genotyped 10 individuals in duplicate using both saliva- and blood-derived DNA. The performance of blood- versus saliva-derived DNA was compared using genotyping call rate, which reflects both the quantity and quality of genotyping per sample and the “GCScore,” an Illumina genotyping quality score, which is a measure of DNA quality. We also compared genotype calls and GCScores for the 10 sample pairs. Call rates were assessed for each sample individually. For the GWAS samples, we compared data according to source of DNA and center of origin. We observed high concordance in genotyping quality and quantity between the paired samples and minimal loss of quality and quantity of DNA in the saliva samples in the large GWAS sample, with the blood samples showing greater variation between centers of origin. This large data set highlights the usefulness of saliva DNA for genotyping, especially in high-density single-nucleotide polymorphism microarray studies such as GWAS. Cancer Epidemiol Biomarkers Prev; 19(3); 794–8
p53 Autoantibodies as Potential Detection and Prognostic Biomarkers in Serous Ovarian Cancer
Authors: Anderson Karen S. , Wong Jessica , Vitonis Allison , Crum Christopher P. , Sluss Patrick M. , LaBaer Joshua , Cramer Daniel 
Published: March 2010

AbstractBackground: This study examined the value of serum p53 autoantibodies (p53-AAb) as detection and prognostic biomarkers in ovarian cancer.Methods: p53-AAb were detected by ELISA in sera obtained preoperatively from women undergoing surgery for a pelvic mass. This group included women subsequently diagnosed with invasive serous ovarian cancer (n = 60), nonserous ovarian cancers (n = 30), and women with benign disease (n = 30). Age-matched controls were selected from the general population (n = 120). Receiver operating characteristic curves were constructed to compare the values of p53-AAb, CA 125, and HE4 as a screening biomarker. Kaplan-Meier curves and Cox proportional hazards modeling were used to assess its prognostic value on survival.Results: p53-AAb were detected in 25 of 60 (41.7%) of serous cases, 4 of 30 (13.3%) nonserous cases, 3 of 30 (10%) benign disease cases, and 10 of 120 (8.3%) controls (combined P = 0.0002). p53-AAb did not significantly improve the detection of cases [area under the curve (AUC), 0.69] or the discrimination of benign versus malignant disease (AUC, 0.64) compared with CA 125 (AUC, 0.99) or HE4 (AUC, 0.98). In multivariate analysis among cases, p53-AAb correlated only with a family history of breast cancer (P = 0.01). Detectable p53 antibodies in pretreatment sera were correlated with improved overall survival (P = 0.04; hazard ratio, 0.57; 95% confidence interval, 0.33-0.97) in serous ovarian cancer.Conclusions: Antibodies to p53 are detected in the sera of 42% of patients with advanced serous ovarian cancer.Impact: Although their utility as a preoperative diagnostic biomarker, beyond CA 125 and HE4, is limited, p53-AAb are prognostic for improved overall survival. Cancer Epidemiol Biomarkers Prev; 19(3); 859–68
Influence of Nurses on Compliance with Breast Screening Recommendations in an Organized Breast Screening Program
Authors: Chiarelli Anna M. , Majpruz Vicky , Brown Patrick , Theriault Marc , Edwards Sarah , Shumak Rene , Mai Verna 
Published: March 2010

AbstractBackground: Evidence from breast screening trials has shown that a significant reduction in breast cancer mortality from screening can be achieved by regular attendance. Few studies have evaluated the influence of nurses on compliance with breast screening recommendations.Methods: The cohort included 157,788 women ages 50 to 69 years who were screened at 1 of 9 regional cancer centers or 57 affiliated centers with nurses or 26 affiliated centers without nurses between January 1, 2002, and December 31, 2002, within the Ontario Breast Screening Program. These women were followed up prospectively for at least 30 months to compare compliance for annual and biennial screening recommendations among women who attended centers with and without nurses. The associations between type of screening center and the odds of compliance were modeled using mixed-effect logistic regression models. All P values are two-sided.Results: Women attending a regional cancer center [odds ratios (OR), 1.96; 95% confidence interval (95% CI), 1.07-3.58] or affiliated center with nurses (OR, 1.75; 95% CI, 1.38-2.22) were significantly more likely to return within 18 months of their annual screening recommendation than women attending affiliated centers without nurses. In addition, women attending regional cancer centers (OR, 2.28; 95% CI, 1.34-3.89) or affiliated centers with nurses (OR, 2.30; 95% CI, 1.86-2.83) were significantly more likely to make a timely return within the recommended biennial screening interval of between 18 and 30 months.Conclusions: Breast screening programs should consider methods of integrating educational activities as provided by the nurses to improve compliance with screening. Cancer Epidemiol Biomarkers Prev; 19(3); 697–706
Low to Moderate Alcohol Intake Is Not Associated with Increased Mortality after Breast Cancer
Authors: Flatt Shirley W. , Thomson Cynthia A. , Gold Ellen B. , Natarajan Loki , Rock Cheryl L. , Al-Delaimy Wael K. , Patterson Ruth E. , Saquib Nazmus , Caan Bette J. , Pierce John P. 
Published: March 2010

Abstract
Background: Both alcohol consumption and obesity have been linked with breast cancer morbidity and mortality. An inverse association between alcohol intake and obesity suggests possible confounding between these variables (and perhaps other factors) with breast cancer outcomes.
Methods: Alcohol intake (beer, wine, spirits, and total) was examined in 3,088 women previously diagnosed and treated for breast cancer within an intervention trial that targeted vegetables, fiber, and fat but not alcohol or weight loss. Factors associated with baseline alcohol intake were included in Cox proportional hazards models for recurrence and mortality.
Results: Alcohol intake was significantly associated with higher education and physical activity levels. Neither light alcohol intake nor obesity was significantly associated with breast cancer recurrence, but moderate alcohol intake &gt;300 g/mo was protective against all-cause mortality (hazard ratio, 0.69; 95% confidence intervals, 0.49-0.97) in a proportional hazards model adjusted for obesity. Obese women were 61% more likely to be nondrinkers than drinkers, and 76% more likely to be light drinkers than moderate/heavy drinkers. In nonobese women, alcohol intake &gt;10 g/mo was associated with lower risk of all-cause mortality (hazard ratio, 0.68; 95% confidence intervals, 0.51-0.91).
Conclusion: Light alcohol intake, regardless of body weight, did not increase the risk of breast cancer recurrence or all-cause mortality in this cohort of middle-aged women previously diagnosed with breast cancer. Alcohol intake was associated with other favorable prognostic indicators, which may explain its apparent protective effect in nonobese women. Cancer Epidemiol Biomarkers Prev; 19(3); 681–8
Androgen Receptor CAG Repeat Length and Risk of Biliary Tract Cancer and Stones
Authors: Meyer Tamra E. , O'Brien Thomas G. , Andreotti Gabriella , Yu Kai , Li Qizhai , Gao Yu-Tang , Rashid Asif , Shen Ming-Chang , Wang Bing-Sheng , Han Tian-Quan , Zhang Bai-He , Niwa Shelley , Fraumeni Joseph F. , Hsing Ann W. 
Published: March 2010

Abstract
Biliary tract cancers, encompassing cancers of the gallbladder, extrahepatic bile ducts, and ampulla of Vater, are rare but highly fatal. Gallstones represent the major risk factor for biliary tract cancer, and share with gallbladder cancer a female predominance and an association with reproductive factors and obesity. Although estrogens have been implicated in earlier studies of gallbladder cancer, there are no data on the role of androgens. Because intracellular androgen activity is mediated through the androgen receptor (AR), we examined associations between AR CAG repeat length [(CAG)n] and the risk of biliary tract cancers and stones in a population-based study of 331 incident cancer cases, 837 gallstone cases, and 750 controls from Shanghai, China, where the incidence rates for biliary tract cancer are rising sharply. Men with (CAG)n &gt;24 had a significant 2-fold risk of gallbladder cancer [odds ratio (OR), 2.00; 95% confidence interval (CI), 1.07-3.73], relative to those with (CAG)n ≤ 22. In contrast, women with (CAG)n &gt;24 had reduced gallbladder cancer risk (OR, 0.69; 95% CI, 0.43-1.09) relative to those with (CAG)n ≤ 22; P interaction sex = 0.01, which was most pronounced for women ages 68 to 74 (OR, 0.48; 95% CI, 0.25-0.93; P interaction age = 0.02). No associations were found for bile duct cancer or gallstones. Reasons for the heterogeneity of genetic effects by gender and age are unclear but may reflect an interplay between AR and the levels of androgen as well as estrogen in men and older women. Further studies are needed to confirm these findings and clarify the mechanisms involved. Cancer Epidemiol Biomarkers Prev; 19(3); 787–93
Distribution and Hepatocellular Carcinoma–Related Viral Properties of Hepatitis B Virus Genotypes in Mainland China: A Community-Based Study
Authors: Yin Jianhua , Zhang Hongwei , He Yongchao , Xie Jiaxin , Liu Shijian , Chang Wenjun , Tan Xiaojie , Gu Chunying , Lu Wei , Wang Hongyang , Bi Shengli , Cui Fuqiang , Liang Xiaofeng , Schaefer Stephan , Cao Guangwen 
Published: March 2010

Abstract
Introduction: Hepatitis B virus (HBV) genotypes, replication status, and mutations have been associated with the risk of hepatocellular carcinoma (HCC). Our aim was to study the distribution and HCC-related viral properties of HBV genotypes/subgenotypes in Mainland China.
Methods: A multistage cluster probability sampling method was applied to select 81,775 participants between 1 and 59 years at 160 national disease surveillance points. We examined hepatitis B surface antigen, HBV genotypes and subgenotypes, hepatitis B e antigen, viral load, and mutations in the PreS and core promoter regions of HBV genome.
Results: HBV subgenotypes B2 (27.3%), C1 (10.7%), and C2 (58.0%) were predominant. Genotype D (D1, 80.8%) was frequent in the Uygur. We identified a new subgenotype, C9, mainly in Tibetans. Compositions of subgenotypes B2 and C1 and genotype mixture increased from the North to Central South, which was consistently associated with the increasing prevalence of hepatitis B surface antigen. Hepatitis B e antigen positivity and viral loads were higher in the young with genotype B and declined more rapidly with increasing age than those with genotype C. In contrast to G1896A, PreS deletion, T31C, T1753V, and A1762T/G1764A were more frequent in subgenotype C2 than in subgenotype B2. A1762T/G1764A, T1753V, C1653T, and G1896A, except PreS deletion, consecutively increased with increasing age.
Conclusion: HBV subgenotypes B2, C1, and C2 are endemic in Mainland China. HBV genotype C exhibits less replication activity in the young and harbors higher frequencies of the HCC-associated mutations than genotype B.
Impact: These basic data could help evaluate the association of HBV variations with HCC. Cancer Epidemiol Biomarkers Prev; 19(3); 777–86
Association between Statins and Prostate Tumor Inflammatory Infiltrate in Men Undergoing Radical Prostatectomy
Authors: Bañez Lionel L. , Klink Joseph C. , Jayachandran Jayakrishnan , Lark Amy L. , Gerber Leah , Hamilton Robert J. , Masko Elizabeth M. , Vollmer Robin T. , Freedland Stephen J. 
Published: March 2010

Abstract
Background: Cholesterol-lowering drugs known as statins have been reported to have significant anti-inflammatory properties. Given that inflammation may contribute to prostate cancer progression and that statins may reduce the risk for advanced prostate cancer, we investigated whether statin use was associated with reduced intratumoral inflammation in radical prostatectomy (RP) specimens.
Methods: Inflammation within index tumors of 236 men undergoing RP from 1996 to 2004 was graded by a single pathologist as grade 0 (absent), 1 (mild: ≤10%), and 2 (marked: &gt;10%). Preoperative statin use was analyzed by grouping subjects as statin users or nonusers. Type and dosage of statin was accounted for using dose equivalents with 20 mg simvastatin as reference. Logistic regression was used to determine the association between statin use and intratumoral inflammation controlling for age, race, body mass index, prostate-specific antigen, year of surgery, clinical stage, pathologic Gleason sum, surgical margin status, extracapsular extension, seminal vesicle invasion, prostate weight, time from prostate biopsy to RP, and nonsteroidal anti-inflammatory drug use.
Results: Preoperative statin use was significantly associated with lower risk for any (grade ≥1) intratumoral inflammation (odds ratio, 0.31; 95% confidence interval, 0.10-0.98; P = 0.047) on multivariable analysis, with doses ≥20 mg simvastatin equivalents being more strongly associated (relative to nonuse; odds ratio, 0.22; 95% confidence interval, 0.06-0.79; P = 0.02).
Conclusion: In a cohort of men undergoing RP, statin use was associated with significantly lower risk of any inflammation within prostate tumors.
Impact: Given previous reports that inflammation is associated with advanced prostate cancer, and statin use is associated with decreased prostate cancer progression risk, our findings suggest that inhibition of inflammation within tumors may be a potential mechanism for purported anti–prostate cancer properties of statins. Cancer Epidemiol Biomarkers Prev; 19(3); 722–8