bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impairment of cobalt-induced riboflavin biosynthesis in aDebaryomyces hanseniimutant
Authors: Seda-Miró Jasmine M. , Arroyo-González Nancy , Pérez-Matos Ana , Govind Nadathur S. 
Published: November 2007

Flavinogenic yeasts such as Debaryomyces hansenii overproduce riboflavin (RF) in the presence of heavy metals. Growth and RF production were compared between wild-type D. hansenii and a RF production-impaired metal-tolerant ura3 mutant in the presence of sublethal cobalt(II) concentrations. Debaryomyces hansenii (wild type) exhibits an extended lag phase with an increase in RF synthesis. Supplementation of exogenous uracil shortened the lag phase at the highest concentration of cobalt(II) used, suggesting that uracil has a possible role in metal acclimation. The D. hansenii ura3 mutant isolated by chemical mutagenesis exhibited a higher level of metal tolerance, no extended lag phase, and no marked increase in RF synthesis. Transformation of the mutant with the URA3 gene isolated from Saccharyomyces cerevisiae or D. hansenii did not restore wild-type characteristics, suggesting a second mutation that impairs RF oversynthesis. Our results demonstrate that growth, metal sensitivity, and RF biosynthesis are linked.
Amino acid pool composition of the basidiomyceteCoprinus cinereus
Authors: Ulrich Cynthia E. , Gathman Allen C. , Lilly Walt W. 
Published: November 2007

The leaf-litter fungus Coprinus cinereus maintains a pool of free amino acid in its mycelium. When the organism is grown under conditions of high nitrogen availability with 13.2 mmol·L–1l-asparagine as the nitrogen source, the primary constituents of this pool are glutamine, alanine, and glutamic acid. Together these 3 amino acids comprise approximately 70% of the pool. Nitrogen deprivation reduces the size of the free amino acid pool by 75%, and neither a high concentration of ammonium nor a protein nitrogen source support a similar pool size as l-asparagine. Nitrogen deprivation also reduces the concentration of glutamine to the pool while increasing glutamate. Concomitant with this shift is a marked increase in mycelial ammonium.
Suggestions for stream based parallel systems in Ada
Authors: Ward M. , Audsley N. C. 
Published: November 2007

Ada provides good support for the implementation of dependable, real-time, control systems. However, its support for other styles of systems is not as good. This paper explores the support available for implementing parallel, stream based systems.
The paper presents an implementation of an image manipulation system which highlights deficiencies in the support for such systems in the Ada language. Two additional semantics are proposed for addition to the Ada language which will provide for the needs of these systems. The broadcast semantic allows the same data to be written to several POs simultaneously. The guarded protected function semantic permits several readers to wait on an entry and simultaneously read data from the PO.
The automation of introductory computer science courses
Authors: Nievergelt Jurg , Reingold Edward M. , Wilcox Thomas R. 
Published: November 2007

In response to a large (currently 2000 students per semester) and increasing enrollment in introductory computer science courses, we have started a project to automate these courses on the PLATO IV Computer-Based Education system at the University of Illinois. The key components of our automated course are:
1. a library of lessons, covering several programming languages, computing techniques, and application areas
2. a completely self-contained interactive programming system for the preparation, execution and debugging of programs written by students in any of the languages covered by the lessons
3. a conversational advice-giving and information retrieval system to guide the student through the library of lessons, based on his goals and past performance.
The goals and current status of this project are described.
Kensho
Authors: Horey James , Maccabe Arthur B. , Mielke Angela 
Published: November 2007

Recent research on sensor network programming architectures has managed to alleviate many common programming burdens, but has not fully addressed the problems associated with tasking and deployment. This has impeded the development of new multi-purpose sensor networks that require new software abstractions and mechanisms.
We present the design of a new software architecture for sensor networks that provides abstractions to explicitly address the issues of tasking and deployment. We also present an initial implementation of our architecture in simulation to investigate the potential memory overheads. Finally, we present a mobile tracking application to demonstrate how to use the abstractions provided by our architecture.
(algorithms)
Authors: Curtis Pavel 
Published: November 2007

I have not been deluged with submissions for this column. I've gotten a few, but not enough to make it easy to put out another issue each quarter. Let me therefore repeat my charter:
The (algorithms) department consists of articles that fit into one or more of three broad categories:
• Annotated implementations of interesting and relevant algorithms; they should make particularly good or novel use of the unique features of the Lisp family of programming languages (e.g., closures, continuations, code as data, polymorphism),
• Annotated implementations of algorithms whose subject matter is the Lisp family of languages (e.g., code analysis tools, iteration facilities, generic arithmetic), and
• Discussion of performance issues, bench-marking, or implementation experiences for interesting algorithms written in or about the Lisp family of languages.
Implementing queues in Lisp
Authors: Norvig Peter , Waters Richard C. 
Published: November 2007

A queue is a data structure where items are entered one at a time and removed one at a time in the same order---i.e., first in first out. They are the same as stacks except that in a stack, items are removed in the reverse of the order they are entered---i.e., last in first out. Queues are most precisely described by the functions that act on them:
(make-queue) Creates and returns a new empty queue.
Predicting link quality using supervised learning in wireless sensor networks
Authors: Wang Yong , Martonosi Margaret , Peh Li-Shiuan 
Published: November 2007

Routing protocols in sensor networks maintain information on neighbor states and potentially many other factors in order to make informed decisions. Challenges arise both in (a) performing accurate and adaptive information discovery and (b) processing/analyzing the gathered data to extract useful features and correlations. To address such challenges, this paper explores using supervised learning techniques to make informed decisions in the context of wireless sensor networks.
We investigate the design space of both offline learning and online learning and use link quality estimation as a case study to evaluate their effectiveness. For this purpose, we present MetricMap, a metric-based collection routing protocol atop MintRoute that derives link quality using classifiers learned in the training phase, when the traditional ETX approach fails. The offline learning approach is evaluated on a 30-node sensor network testbed, and our results show that MetricMap can achieve up to 300% improvement over MintRoute in data delivery rate for high data rate situations, with no negative impact on other performance metrics. We also explore the possibility of using online learning in this paper.
Evaluating curricula for the teaching of programming
Authors: Ragsdale Ronald G. 
Published: November 2007

Despite the great and continuing interest in methods of effective teaching of computer science concepts, especially programming, there is little hard data to back up the opinions that are so vigorously expressed. Moreover, most of those studies that have attempted to investigate programming instruction have been sufficiently flawed so as to render them of little use.
The first section of this paper deals with many of the flaws commonly found in studies of instruction in programming. These include non-random assignment of subjects, assuming identical instruction to different groups, experimenter bias, use of "available resources", short experimental treatments, home grown tests, and questionable analysis techniques.
The second section contains a description of the principles of good experimental design, using the concepts of internal and external validity. An experiment usually requires a compromise between the internal validity, which relates to control of experimental conditions, and the external validity, which has to do with the generalizability of the results.
The final section contains conclusions concerning initial steps that might be taken to rectify the problem caused by a lack of valid data. These steps include better and more objective quantification of the attributes of good programs and more integrative techniques for analyzing the results of multiple studies.
Longitudinal Study of Insulin-like Growth Factor, Insulin-like Growth Factor Binding Protein-3, and their Polymorphisms: Risk of Neoplastic Progression in Barrett's Esophagus
Authors: Siahpush Sid H. , Vaughan Thomas L. , Lampe Johanna N. , Freeman Robert , Lewis SKay , Odze Robert D. , Blount Patricia L. , Ayub Kamran , Rabinovitch Peter S. , Reid Brian J. , Chen Chu 
Published: November 2007

AbstractBackground: Insulin-like growth factor-I (IGF-I) is a potent mitogen. IGF-I and its main binding protein, IGF binding protein-3 (IGFBP-3), and their polymorphisms have been investigated in relation to risk of many cancers, but not esophageal adenocarcinoma.Materials and Methods: We used data and specimens from a longitudinal study of persons with Barrett's esophagus (n = 344; median, 5.4 years follow up) to determine whether baseline serum concentrations of IGF-I and IGFBP-3 and associated polymorphisms were related to the risk of developing esophageal adenocarcinoma or flow cytometric abnormalities.Results: Overall, circulating concentrations of IGF-I and IGBP-3 were not associated with risk of esophageal adenocarcinoma or flow cytometric abnormalities, with the exception of an approximate tripling of risk of aneuploidy among participants with higher IGFBP-3 levels [above median; adjusted hazard ratio (HR) comparing subjects with levels lower than median versus higher of equal to median, 2.7; 95% confidence interval (95% CI), 1.2-6.0; P = 0.01]. Genotypic analyses revealed that persons with the IGF-I [cytosine-adenine (CA)]19 or the IGFBP-3 A-202C C allele were associated with lower circulating concentrations of IGF-I (Ptrend = 0.01) and IGFBP-3 (Ptrend = 0.002), respectively. Persons with two copies of the IGF-I receptors 2-bp deletion allele had a nonsignificant 2-fold increased risk of tetraploidy (HR, 2.3; 95% CI, 0.9-5.9; Ptrend = 0.11). After adjustment for IGFBP-3 levels, participants carrying two IGFBP-3 C alleles had a significantly higher risk of developing aneuploidy (HR, 3.8; 95% CI, 1.0-14.0; Ptrend = 0.04) than carriers of A alleles; whereas no associations were observed between the outcomes studied and the IGF-I receptors AGG trinucleotide repeat polymorphism at position 97.Conclusion: Our findings, although based on a relatively small number of outcomes and subject to several limitations, indicate a potential role of the complex IGF system in neoplastic progression among persons with Barrett's esophagus. (Cancer Epidemiol Biomarkers Prev 2007;16(11):2387–96)
No Effect of Exercise on Colon Mucosal Prostaglandin Concentrations: A 12-Month Randomized Controlled Trial
Authors: Abrahamson Page E. , King Irena B. , Ulrich Cornelia M. , Rudolph Rebecca E. , Irwin Melinda L. , Yasui Yutaka , Surawicz Christina , Lampe Johanna W. , Lampe Paul D. , Morgan Angela , Sorensen Bess E. , Ayub Kamran , Potter John D. , McTiernan Anne 
Published: November 2007

Abstract
Background: Epidemiologic studies provide evidence that exercise is associated with reduced risk of colon cancer. Exercise may exert protective effects on the colon by influencing prostaglandin production. We hypothesized that an exercise intervention would decrease prostaglandin E2 concentrations and increase prostaglandin F2α in colon biopsies compared with controls.
Methods: A 12-month randomized controlled trial testing the effects of exercise on colon mucosal prostaglandin concentrations was conducted in men (n = 95) and women (n = 89). The exercise intervention included moderate-to-vigorous aerobic activity, 60 min/d, 6 days/wk versus controls. Prostaglandin E2 and F2α concentrations were measured in colon biopsies using an enzyme-linked immunoassay at baseline and at 12 months to assess changes in mean concentration for each group.
Results: Baseline colon prostaglandin E2 and F2α concentrations were not correlated with age, race, education, family history of colon cancer, previous polyps, body size, diet, smoking, nonsteroidal antiinflammatory drug use, metabolic factors, or sex hormone levels. For both men and women, the exercise and control groups showed no change in mean prostaglandin E2 or F2α between the baseline and 12-month biopsies. There was no difference in mean prostaglandin concentrations between exercisers and controls when exercisers were grouped by level of intervention adherence. Results were not modified by baseline age, body mass index, percentage of body fat, nonsteroidal antiinflammatory drug use, history of adenomatous polyps, or family history of colon cancer.
Conclusion: A 12-month moderate-to-vigorous intensity aerobic exercise intervention did not result in significant changes in colon mucosal prostaglandin concentrations. (Cancer Epidemiol Biomarkers Prev 2007;16(11):2351–6)
Ataxia Telangiectasia-Mutated Gene Is a Possible Biomarker for Discrimination of Infiltrative Deep Penetrating Nevi and Metastatic Vertical Growth Phase Melanoma
Authors: Roesch Alexander , Becker Bernd , Bentink Stefan , Spang Rainer , Vogl Annegret , Hagen Ilja , Landthaler Michael , Vogt Thomas 
Published: November 2007

Abstract
The deep penetrating nevus (DPN) is a variant of benign melanocytic nevus with clinical and histologic features mimicking vertical growth phase, nodular malignant melanoma (NMM). Because fatal misdiagnosis such as NMM occurs in 29% to 40% of the DPN, molecular differentiation markers are highly desirable. Beyond the clinical demand for precise diagnosis and diagnosis-adapted, preventive therapeutic strategies, the DPN represents a valuable natural model for melanocytic invasion without metastatic potential that per se deserves further investigations. In the present study, at first, we used a genome-wide, microarray-based approach to systematically prescreen for possible molecular markers differentially expressed between selected cases of typical DPN (n = 4) and metastatic NMM controls (n = 4). Gene expression profiling was done on Affymetrix Human X3P microarrays. Of the 47,000 genes spotted, we identified a list of 227 transcripts, which remained significantly regulated at a false discovery rate of 5%. Subsequently, we verified the expression of a subset of the most interesting transcripts in a larger immunohistochemical series (DPN, n = 17; NMM, n = 16). Of these transcripts, three were selected for immunohistochemical confirmation: tissue inhibitor of metalloproteinase-2, tumor protein D52, and ataxia telangiectasia-mutated gene (ATM). Additional criteria for selection from the list of 227 significantly regulated transcripts were grouping into functional Ingenuity networks and a known melanoma- or cancer-relevant function. Following these criteria, we detected a highly significant up-regulation of ATM transcription in NMM, which was also mirrored by ATM protein up-regulation. In contrast to the other markers, ATM particularly might serve as a suitable diagnostic and reliable discriminator of DPN/NMM because ATM immunoreactivity also showed a reliable staining consistency within all samples of both entities. (Cancer Epidemiol Biomarkers Prev 2007;16(11):2486–90)
Evaluation of the Association with Cervical Cancer of Polymorphisms in Syndecan-1, a Heparan Sulfate Proteoglycan Involved with Viral Cell Entry
Authors: Yu Kelly J. , Bashirova Arman , Madeleine Margaret M. , Cheng Jie , Johnson Lisa G. , Schwartz Stephen M. , Carrington Mary , Hildesheim Allan 
Published: November 2007

Abstract
Infection with 1 of ∼15 oncogenic human papillomaviruses is known to be linked to the development of all histologic forms of cervical cancer. We evaluated whether polymorphisms in syndecan-1 (SDC-1), a gene whose protein product is believed to be involved in human papillomavirus entry into epithelial cells, were associated with histologic subtypes of cervical cancer. A total of 293 in situ/invasive adenocarcinoma cases, 260 in situ/invasive squamous cell carcinoma cases, and 478 controls from two studies conducted in the Eastern United States and Seattle area were evaluated. DNA from peripheral blood was used for testing. We sequenced 5 exons and 60 nucleotides upstream of the start codon for SDC-1 in a random subset of 50 cases and 50 controls from the Eastern U.S. Study and identified two polymorphisms (E84E, rs2230924 and Pro-27 C → T, rs11544860). PCR-based testing was done to evaluate risk associated with these two polymorphisms. Polymorphisms of SDC-1 were not associated with risk of squamous cell carcinomas of the cervix. Similarly, there was no evidence for an association between SDC-1 exon 3 polymorphisms and risk of cervical adenocarcinomas. A marginally significant increase in risk of cervical adenocarcinoma was associated with the presence of the Pro-27 polymorphism (pooled odds ratios, 1.6; 95% confidence intervals, 0.99-2.6), an effect that was restricted to the Eastern U.S. Study. Our results indicate a lack of association between SDC-1 polymorphisms and risk of squamous cell carcinomas of the cervix. An association between SDC-1 Pro-27 polymorphism and cervical adenocarcinoma cannot be ruled out. (Cancer Epidemiol Biomarkers Prev 2007;16(11):2504–8)
Nicotine and Carcinogen Exposure with Smoking of Progressively Reduced Nicotine Content Cigarette
Authors: Benowitz Neal L. , Hall Sharon M. , Stewart Susan , Wilson Margaret , Dempsey Delia , Jacob Peyton 
Published: November 2007

Abstract
Background: Reducing the nicotine content of cigarettes to make them non-addictive has been widely discussed as a potential strategy for tobacco regulation. A major concern with nicotine reduction is that smokers will compensate for reduced nicotine by smoking more cigarettes and/or smoking more intensively, thereby increasing their exposure to tobacco smoke toxins. This study examined whether gradual reduction in nicotine exposure increases exposure to tobacco smoke toxins.
Methods: This 10-week longitudinal study of 20 healthy smokers involved smoking their usual brand followed by different types of research cigarettes with progressively lower nicotine content, each smoked for 1 week. Subjects were followed for 4 weeks after returning to smoking their usual brand (or quitting). Smoking behaviors, chemical biomarkers of tobacco smoke exposure, and cardiovascular effect biomarkers were measured.
Findings: Intake of nicotine declined progressively as the nicotine content of cigarettes was reduced, with little evidence of compensation. Cigarette consumption and markers of exposure to carbon monoxide and polycyclic aromatic hydrocarbons, as well as cardiovascular biomarkers remained stable, whereas urinary 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanol excretion decreased. Twenty-five percent of participants had spontaneously quit smoking 4 weeks after completing the research cigarette taper.
Implications: Our findings with reduced nicotine content cigarettes differ from those of commercial low yields for which compensatory smoking for lower nicotine delivery is substantial. Our data suggest that the degree of nicotine dependence of smokers can be lowered without increasing their exposure to tobacco smoke toxins. Gradual reduction of nicotine content of cigarettes seems to be feasible and should be further evaluated as a national tobacco regulatory strategy. (Cancer Epidemiol Biomarkers Prev 2007;16(11):2479–85)
BRCA1andBRCA2Mutations in an Asian Clinic-based Population Detected Using a Comprehensive Strategy
Authors: Ang Peter , Lim Irene H.K. , Lee Tze-Chuen , Luo Jie-Ting , Ong Danny C.T. , Tan Puay Hoon , Lee Ann S.G. 
Published: November 2007

AbstractBackground and objective: Genetic testing for germ line mutations in the BRCA1 and BRCA2 genes for some families at high risk for breast and/or ovarian cancer may yield negative results due to unidentified mutations or mutations with unknown clinical significance. We aimed to accurately determine the prevalence of mutations in these genes in an Asian clinic-based population by using a comprehensive testing strategy.Materials and Methods: Ninety-four subjects from 90 families were accrued from risk assessment clinics. In addition to conventional mutational screening of BRCA1 and BRCA2, multiplex ligation-dependent probe amplification for the detection of large genomic rearrangements, evaluation of splice site alterations using transcript analysis and SpliceSiteFinder prediction, and analysis of missense mutations of unknown significance by multiple sequence alignment, PolyPhen analysis, and comparison of Protein Data Bank structures were incorporated into our testing strategy.Results: The prevalence rates for clearly deleterious BRCA1 and BRCA2 mutations were 6.7% (6 of 90) and 8.9% (8 of 90), respectively, or 7.8% (7 of 90) and 11.1% (10 of 90), respectively, by including missense mutations predicted to be deleterious by computational analysis. In contrast to observations from European and American populations, deleterious mutations in BRCA2 (10 families) were more common than for BRCA1 (7 families). Overall, the frequency of mutations was 12.2% (n = 11) by conventional screening. However, by including deleterious mutations detected using multiplex ligation-dependent probe amplification (n = 1), transcript analysis (n = 2), and computational evaluation of missense mutations (n = 3), the frequency increased substantially to 18.9%. This suggests that the comprehensive strategy used is effective for identifying deleterious mutations in Asian individuals at high risk for breast and/or ovarian cancer. (Cancer Epidemiol Biomarkers Prev 2007;16(11):2276–84)
Cholesterol-Lowering Drugs and Advanced Prostate Cancer Incidence in a Large U.S. Cohort
Authors: Jacobs Eric J. , Rodriguez Carmen , Bain Elizabeth B. , Wang Yiting , Thun Michael J. , Calle Eugenia E. 
Published: November 2007

Abstract
Background: 3-Hydroxy-3-methylglutaryl CoA reductase inhibitors, commonly known as statins, account for the great majority of cholesterol-lowering drug use in the United States. Long-duration statin use was associated with substantially reduced risk of advanced prostate cancer in a recent large prospective study.
Methods: We examined the association between use of cholesterol-lowering drugs and prostate cancer incidence by disease stage and grade among 55,454 men in the Cancer Prevention Study II Nutrition Cohort. Proportional hazards modeling was used to calculate RRs.
Results: During follow-up from 1997 to 2003, we identified 3,413 cases of incident prostate cancer, including 317 cases of advanced prostate cancer. After adjustment for age, history of prostate-specific antigen testing, and other potential prostate cancer risk factors, current use of cholesterol-lowering drugs for 5 or more years was not associated with overall prostate cancer incidence (multivariate adjusted rate ratio, 1.06; 95% confidence interval, 0.93-1.20), but was associated with a marginally statistically significant reduction in risk of advanced prostate cancer (rate ratio, 0.60; 95% confidence interval, 0.36-1.00).
Conclusion: These results provide some support for the hypothesis that long-term statin use is associated with reduced risk of advanced prostate cancer. (Cancer Epidemiol Biomarkers Prev 2007;16(11):2213–7)