bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of a Newly Identified 35-Amino-Acid Component of the Vaccinia Virus Entry/Fusion Complex Conserved in All Chordopoxviruses
Authors: Satheshkumar P. S. , Moss Bernard 
Published: October 2009

ABSTRACT
The original annotation of the vaccinia virus (VACV) genome was limited to open reading frames (ORFs) of at least 65 amino acids. Here, we characterized a 35-amino-acid ORF (O3L) located between ORFs O2L and I1L. ORFs similar in length to O3L were found at the same genetic locus in all vertebrate poxviruses. Although amino acid identities were low, the presence of a characteristic N-terminal hydrophobic domain strongly suggested that the other poxvirus genes were orthologs. Further studies demonstrated that the O3 protein was expressed at late times after infection and incorporated into the membrane of the mature virion. An O3L deletion mutant was barely viable, producing tiny plaques and a 3-log reduction in infectious progeny. A mutant VACV with a regulated O3L gene had a similar phenotype in the absence of inducer. There was no apparent defect in virus morphogenesis, though O3-deficient virus had low infectivity. The impairment was shown to be at the stage of virus entry, as cores were not detected in the cytoplasm after virus adsorption. Furthermore, O3-deficient virus did not induce fusion of infected cells when triggered by low pH. These characteristics are hallmarks of a group of proteins that form the entry/fusion complex (EFC). Affinity purification experiments demonstrated an association of O3 with EFC proteins. In addition, the assembly or stability of the EFC was impaired when expression of O3 was repressed. Thus, O3 is the newest recognized component of the EFC and the smallest VACV protein shown to have a function.
Building bridges
Authors: Westman Hans 
Published: October 2009

What discipline in science, the arts or technology is truly isolated? The more one delves into their mysteries it becomes clear how inter-disciplinary they are. The mind jumps from one impression to the next in determining how existence is constructed. Though the perception may be subjective, it is an experience that is shared by many.
Science, the arts and technology are three separate disciplines, but have more in common than meets the eye. They are different lenses from which to observe reality.
We may see things differently, but if we share our insights, we build bridges and broaden our understanding.
This is the theme for the May 2009 issue of the SIGGRAPH e-quarter "Computer Graphics", emphasizing the importance of collaboration to improve the way computer graphics is used in different ways.
Elizabeth A. Rega, Department of Anatomy, Western University of Heath Sciences and Stuart S. Sumida, Department of Biology, California State University of Heath Sciences, have written an article together entitled "Anatomical Considerations in Facial Motion Capture", stressing the importance of understanding inherent traits of human facial expression to improve motion capture performance.
"iVisit Agitating for the Evolution of Fixed-mobile Tele-presence and Augmented Reality" by Orang Dialameh, CEO of iVisit, LLC introduces how current mobile video-calling software, spearheaded by CU-SeeMe creator Tim Dorcey, is taking advantage of the HTC (High Tech Computers) smart phone and pocket PC devices to assist doctors in meeting and treating patients remotely and helping persons who are visually impaired.
In the article "A Survey of BRDF Models for Computer Graphics" Murat Kurt, Ege University, International Computer Institute, Turkey and Dave Edwards, University of Utah, Salt Lake City, Utah, survey the most popular BRDF representations introduced so far and analyzed the most recent trends in this area. This article follows up an earlier article entitle "Representing BRDFs using SOMs and MANs", also written by Murat Kurt together with Muhammed Gókhan Cinsdikici, Ege University, International Computer Institute, Turkey.
Contributor Carlos D. Correa has written an informative article entitled "Visualizing What Lies Inside" for VisFiles, a very interesting read. My thanks to Kwan-Liu Ma for his continued solicitation of meaningful content for this section of the newsletter.
In conclusion, Jack Lew, Director of Collaborations at the Center for Emerging Media, University of Central Florida, comes full circle through his submission to Education entitled "Connecting the Dots by Crossing Borders", sharing how he, in his new position, sees scientists, artists and technologists collaborating and exploring new solutions in this field we broadly identify as computer graphics. Jack also contributed with the organizational chart used in the design of this issue's cover illustration.
Comparing the performance of concurrent linked-list implementations in Haskell (abstract only)
Authors: Sulzmann Martin , Lam Edmund S.L. , Marlow Simon 
Published: October 2009

Haskell has a rich set of synchronization primitives for implementing shared-state concurrency abstractions, ranging from the very high level (Software Transactional Memory) to the very low level (mutable variables with atomic read-modifywrite).
In this paper we perform a systematic comparison of these different concurrent programming models by using them to implement the same abstraction: a concurrent linked-list. Our results are somewhat surprising: there is a full two orders of magnitude difference in performance between the slowest and the fastest implementation. Our analysis of the performance results gives new insights into the relative performance of the programming models and their implementation.
Finally, we suggest the addition of a single primitive which in our experiments improves the performance of one of the STM-based implementations by more than a factor of 7.
Aberrant Methylation of RASSF1A in Plasma DNA Before Breast Cancer Diagnosis in the Breast Cancer Family Registry
Authors: Yazici Hulya , Terry Mary Beth , Cho Yoon Hee , Senie Ruby T. , Liao Yuyan , Andrulis Irene , Santella Regina M. 
Published: October 2009

Abstract
In addition to classic genetic mechanisms such as deletions and mutations, growth regulatory genes can be inactivated via methylation of cytosine-residues in their promoter regions. Hypermethylation of promoter CpG islands is now recognized as an important and early event in carcinogenesis. Detection of methylated DNA in serum or plasma has been suggested to be a marker for early cancer development. We examined methylation changes in RASSF1A, a growth regulatory gene in plasma DNA from blood collected before diagnosis from women with breast cancer and from controls. Samples were from two sets of subjects, 28 women with breast cancer and 10 of their unaffected siblings, and 33 women with breast cancer and 29 age- and ethnicity-matched population-based controls. Using methylation specific PCR, we found 11 of 61 (18%) cases were positive for methylation of RASSF1A in their plasma DNA collected before diagnosis. Two of 10 healthy high-risk sibling controls (20%) had plasma DNA positive for RASSF1A methylation in their plasma DNA compared with 0 of 29 (0%) population-based controls. Tumor tissue was available for 12 cases and all were positive for RASSF1A methylation. These results, if replicated, suggest that aberrant promoter hypermethylation in serum/plasma DNA may be common among high-risk women and may be present years before cancer diagnosis. (Cancer Epidemiol Biomarkers Prev 2009;18(10):2723–5)
Association of Area Socioeconomic Status and Breast, Cervical, and Colorectal Cancer Screening: A Systematic Review
Authors: Pruitt Sandi L. , Shim Matthew J. , Mullen Patricia Dolan , Vernon Sally W. , Amick Benjamin C. 
Published: October 2009

Abstract
Background: Although numerous studies have examined the association of area socioeconomic status (SES) and cancer screening after controlling for individual SES, findings have been inconsistent. A systematic review of existing studies is timely to identify conceptual and methodologic limitations and to provide a basis for future research directions and policy.
Objective: The objectives were to (a) describe the study designs, constructs, methods, and measures; (b) describe the independent association of area SES and cancer screening; and (c) identify neglected areas of research.
Methods: We searched six electronic databases and manually searched cited and citing articles. Eligible studies were published before 2008 in peer-reviewed journals in English, represented primary data on individuals ages ≥18 years from developed countries, and measured the association of area and individual SES with breast, cervical, or colorectal cancer screening.
Results: Of 19 eligible studies, most measured breast cancer screening. Studies varied widely in research design, definitions, and measures of SES, cancer screening behaviors, and covariates. Eight employed multilevel logistic regression, whereas the remainder analyzed data with standard single-level logistic regression. The majority measured one or two indicators of area and individual SES; common indicators at both levels were poverty, income, and education. There was no consistent pattern in the association between area SES and cancer screening.
Discussion: The gaps and conceptual and methodologic heterogeneity in the literature to date limit definitive conclusions about an underlying association between area SES and cancer screening. We identify five areas of research deserving greater attention in the literature. (Cancer Epidemiol Biomarkers Prev 2009;18(10):2579–99)
Cost-Effectiveness of Prophylactic Surgery for Duodenal Cancer in Familial Adenomatous Polyposis
Authors: Greenblatt Wesley H. , Hur Chin , Knudsen Amy B. , Evans John A. , Chung Daniel C. , Gazelle G. Scott 
Published: October 2009

Abstract
Background: Duodenal cancer is the leading cause of cancer death in familial adenomatous polyposis after colorectal cancer. The lifetime risk for developing duodenal cancer is 4% to 10%. Current treatment guidelines recommend endoscopic surveillance with a prophylactic pancreaticoduodenectomy in advanced duodenal polyposis, defined using the Spigelman staging system. Because no clinical trials have assessed this recommendation, a modeling approach was used to evaluate the cost-effectiveness of various treatment strategies.
Methods: A Markov model was constructed to estimate the life expectancy and cost of three different strategies: pancreaticoduodenectomy at Spigelman stage III, pancreaticoduodenectomy at Spigelman stage IV, and pancreaticoduodenectomy at cancer diagnosis. A cohort of 30-year-old familial adenomatous polyposis patients with total colectomies was simulated until age 80. The analysis was from a societal perspective. Extensive sensitivity analysis was performed to assess the impact of model uncertainty on results.
Results: At all stages of polyposis and all ages &lt;80 years, prophylactic surgery at Spigelman stage IV resulted in the greatest life expectancy. Surgery at stage IV was more effective and more expensive than surgery at cancer diagnosis, with an incremental cost of $3,200 per quality-adjusted life year gained. Surgery at stage III was not a viable option. The results were robust to wide variation in model parameters but were sensitive to the post-pancreaticoduodenectomy quality of life score.
Conclusions: Prophylactic pancreaticoduodenectomy at stage IV duodenal polyposis in familial adenomatous polyposis is a cost-effective approach that results in greater life expectancy than surgery at either stage III or cancer diagnosis. (Cancer Epidemiol Biomarkers Prev 2009;18(10):2677–84)
Nicotinic Acetylcholine Receptor β2 Subunit (CHRNB2) Gene and Short-Term Ability to Quit Smoking in Response to Nicotine Patch
Authors: Perkins Kenneth A. , Lerman Caryn , Mercincavage Melissa , Fonte Carolyn A. , Briski Jessica L. 
Published: October 2009

Abstract
Genes coding for nicotinic acetylcholine receptors may influence response to nicotine replacement therapy for smoking cessation. We examined the association of a 3′ untranslated region polymorphism (rs2072661) in the nicotinic acetylcholine receptor β2 subunit (CHRNB2) gene with quitting success in response to nicotine versus placebo patch during a short-term test of patch effects. In a within-subjects cross-over design, smokers of European descent (n = 156) received 21 mg nicotine and placebo patch in counter-balanced order, during two separate 5-day simulated quit attempts, each preceded by a week of ad libitum smoking. Abstinence was assessed daily by CO &lt; 5 ppm. Smokers with the CHRNB2 GG genotype had more days of abstinence during the nicotine versus placebo patch week compared with those with the AG or AA genotypes (P &lt; 0.01). Moreover, nicotine patch increased the probability of quitting on the target quit day, quitting anytime during the patch week, and avoiding relapse among those with the GG genotype but not the AA/AG genotypes, although the nicotine × genotype interaction was significant only for quitting on the target quit day (P &lt; 0.05). Regardless of patch condition, quitting on the target quit day was more likely in those with the GG genotype versus AA/AG genotypes (P &lt; 0.05). Genetic associations were not observed for craving or withdrawal responses to nicotine versus placebo patch. These findings are consistent with previous evidence of association of this variant with smoking cessation and suggest that polymorphisms in the nicotinic acetylcholine receptor β2 subunit gene may influence therapeutic responsiveness to cessation medications. (Cancer Epidemiol Biomarkers Prev 2009;18(10):2608–12)
An Experimental Test of the Effect of Incentives on Recruitment of Ethnically Diverse Colorectal Cancer Cases and Their First-Degree Relatives into a Research Study
Authors: Maxwell Annette E. , Bastani Roshan , Glenn Beth A. , Mojica Cynthia M. , Chang L. Cindy 
Published: October 2009

AbstractBackground: Optimizing participant response rates is important for obtaining representative samples and the timely completion of studies. It is a common practice to use participant incentives to boost response rates, but few studies have systematically examined their effectiveness, particularly among minority groups.Methods: We experimentally tested three incentive strategies for their effectiveness in improving response rates among colorectal cancer cases (n = 3,816) and their relatives (n = 2,353). A 2 × 2 × 2 factorial design compared (a) registered versus first class mail, (b) $5 cash with the initial mailing (yes/no), and (c) $20 promise (yes/no) upon completion of the information form (for cases) or $10 promise (yes/no) upon completion of the baseline survey (for relatives). Outcome measures were provision of contact information on first-degree relatives for cases and completion of the baseline survey for relatives.Results: The response rate among cases was low in all ethnic groups (28-37%) and incentive strategies did not have an effect. Among relatives, the overall baseline survey response rate was 71%, ranging from 66% among Asians to 76% among Whites. Modest absolute increases were observed for payment schedules that included a $5 cash enclosure with the initial mailing in the total sample [odds ratio (OR), 1.65 and 1.47] and among Latinos (OR, 1.94 and 1.74) but not among Asians (OR, 1.61 and 1.55) or African Americans (OR, 1.19 and 1.02). Response rates were not influenced by registered versus first-class mailing.Conclusion: The effects of incentives in this study were modest with some suggestion of differences by ethnic group and type of incentive. (Cancer Epidemiol Biomarkers Prev 2009;18(10):2620–5)
Medical Advances and Racial/Ethnic Disparities in Cancer Survival
Authors: Tehranifar Parisa , Neugut Alfred I. , Phelan Jo C. , Link Bruce G. , Liao Yuyan , Desai Manisha , Terry Mary Beth 
Published: October 2009

Abstract
Background: Although advances in early detection and treatment of cancer improve overall population survival, these advances may not benefit all population groups equally and may heighten racial/ethnic differences in survival.
Methods: We identified cancer cases in the Surveillance, Epidemiology and End Results program, who were ages ≥20 years and diagnosed with one invasive cancer in 1995 to 1999 (n = 580,225). We used 5-year relative survival rates to measure the degree to which mortality from each cancer is amenable to medical interventions (amenability index). We used Kaplan-Meier methods and Cox proportional hazards regression to estimate survival differences between each racial/ethnic minority group relative to Whites, by the overall amenability index, and three levels of amenability (nonamenable, partly amenable, and mostly amenable cancers, corresponding to cancers with 5-year relative survival rate &lt;40%, 40-69%, and ≥70%, respectively), adjusting for gender, age, disease stage, and county-level poverty concentration.
Results: As amenability increased, racial/ethnic differences in cancer survival increased for African Americans, American Indians/Native Alaskans, and Hispanics relative to Whites. For example, the hazard ratios (95% confidence intervals) for African Americans versus Whites from nonamenable, partly amenable, and mostly amenable cancers were 1.05 (1.03-1.07), 1.38 (1.34-1.41), and 1.41 (1.37-1.46), respectively. Asians/Pacific Islanders had similar or longer survival relative to Whites across amenability levels; however, several subgroups experienced increasingly poorer survival with increasing amenability.
Conclusions: Cancer survival disparities for most racial/ethnic minority populations widen as cancers become more amenable to medical interventions. Efforts in developing cancer control measures must be coupled with specific strategies for reducing the expected disparities. (Cancer Epidemiol Biomarkers Prev 2009;18(10):2701–8)
The Association between Skin Characteristics and Skin Cancer Prevention Behaviors
Authors: Wheless Lee , Ruczinski Ingo , Alani Rhoda M. , Clipp Sandra , Hoffman-Bolton Judith , Jorgensen Timothy J. , Liégeois Nanette J. , Strickland Paul T. , Alberg Anthony J. 
Published: October 2009

Abstract
Background: Behaviors such as sunscreen use and wearing sun-protective clothing are thought to prevent certain types of skin cancer and precancerous lesions, but few studies have examined differences in these prevention behaviors by skin type.
Methods: We carried out a cross-sectional study (n = 6,858) nested within a community-based prospective cohort in Washington County, Maryland. We measured the associations between skin type, complexion, freckling, and eye color, and sunscreen and sun-protective clothing use.
Results: The prevalence of regular sunscreen use was 23% and regular sun-protective clothing use was 21%. There were consistent trends indicating those with the most sun-sensitive skin type were most likely to engage in prevention behaviors. For example, compared with those who tan without burning, those who develop blistering sunburns were more likely to use sunscreen [odds ratio (OR), 6.04; 95% confidence interval (95% CI), 2.82-12.95 men; OR, 4.89; 95% CI, 3.34-7.16 women] and sun-protective clothing (OR, 2.87; 95% CI, 1.71-4.80 men; OR, 4.44; 95% CI, 2.88-6.85 women). Health-related characteristics such as body mass index and cigarette smoking were also significantly inversely associated with prevention behaviors.
Conclusion: The overall prevalence of prevention behaviors was low. Those with phenotypic risk factors for skin cancer were most likely to use sunscreen and sun-protective clothing. Those with high-risk skin cancer phenotypes may also be those who are most receptive to skin cancer prevention educational interventions. (Cancer Epidemiol Biomarkers Prev 2009;18(10):2613–9)
Role of Inflammation Gene Polymorphisms on Pain Severity in Lung Cancer Patients
Authors: Reyes-Gibby Cielito C. , Spitz Margaret R. , Yennurajalingam Sriram , Swartz Michael , Gu Jian , Wu Xifeng , Bruera Eduardo , Shete Sanjay 
Published: October 2009

Abstract
Many of the same inflammatory factors that promote tumor growth are also hypothesized to function as pain modulators. There is substantial interindividual variation in pain severity in cancer patients. Therefore, we evaluated 59 single nucleotide polymorphisms in 37 inflammation genes in newly diagnosed non-Hispanic Caucasian lung cancer patients (n = 667) and assessed their association with pain severity. Patients rated their pain “during the past week” on an 11-point numeric scale (0 = “no pain” and 10 = “pain as bad as you can imagine”) at presentation before initiating cancer therapy. Reported analgesic use was abstracted from charts and converted to morphine equivalent daily dose. Results showed that 16% of the patients reported severe pain (score ≥7). Advanced stage of disease [odds ratio (OR), 2.34; 95% confidence interval (95% CI), 1.50-3.65; P = 0.001], age ≤50 years (OR, 2.10; 95% CI, 1.32-3.30; P = 0.002), reports of depressed mood (OR, 3.68; 95% CI, 1.96-6.93; P = 0.001), fatigue (OR, 3.72; 95% CI, 2.36-5.87; P = 0.001), and morphine equivalent daily dose (OR, 1.02; 95% CI, 1.01-1.03) were significantly correlated with severe pain. Controlling for these nongenetic covariates, we found that patients with CC genotypes for PTGS2 exon10+837T&gt;C (rs5275) were at lower risk for severe pain (OR, 0.33; 95% CI, 0.11-0.97) and an additive model for TNFα −308GA (rs1800629; OR, 1.67; 95% CI, 1.08-2.58) and NFKBIA Ex6+50C&gt;T (rs8904) was predictive of severe pain (OR, 0.64; 95% CI, 0.43-0.93). In a multigene analysis, we found a gene-dose effect, with each protective genotype reducing the risk for severe pain by as much as 38%. This study suggests the importance of inflammation gene polymorphisms in modulating pain severity. Additional studies are needed to validate our findings. (Cancer Epidemiol Biomarkers Prev 2009;18(10):2636–42)
Folate Status and Aberrant DNA Methylation Are Associated With HPV Infection and Cervical Pathogenesis
Authors: Flatley Janet E. , McNeir Kristelle , Balasubramani Latha , Tidy John , Stuart Emma L. , Young Tracey A. , Powers Hilary J. 
Published: October 2009

Abstract
Aberrant DNA methylation is a recognized feature of human cancers, and folate is directly involved in DNA methylation via one-carbon metabolism. Previous reports also suggest that folate status is associated with the natural history of human papillomavirus (HPV) infection. A cross-sectional study was conducted to test the hypothesis that folate status and aberrant DNA methylation show a progressive change across stages of cervical pathology from normal cells to cervical cancer. Additionally, we postulated that a gene-specific hypermethylation profile might be used as a predictive biomarker of cervical cancer risk. DNA hypermethylation of seven tumor suppressor genes, global DNA hypomethylation, systemic folate status, and HPV status were measured in 308 women with a diagnosis of normal cervix (n = 58), low-grade cervical intraepithelial neoplasia (CIN1; n = 68), high-grade cervical intraepithelial neoplasia (CIN2, n = 56; and CIN3, n = 76), or invasive cervical cancer (ICC; n = 50). Lower folate status was associated with high-risk HPV infection (P = 0.031) and with a diagnosis of cervical intraepithelial neoplasia or invasive cervical cancer (P &lt; 0.05). Global DNA hypomethylation was greater in women with invasive cervical cancer than all other groups (P &lt; 0.05). A cluster of three tumor suppressor genes, CDH1, DAPK, and HIC1, displayed a significantly increased frequency of promoter methylation with progressively more severe cervical neoplasia (P &lt; 0.05). These findings are compatible with a role for folate in modulating the risk of cervical cancer, possibly through an influence over high-risk HPV infection. DAPK, CDH1, and HIC1 genes are potential biomarkers of cervical cancer risk. (Cancer Epidemiol Biomarkers Prev 2009;18(10):2782–9)