bluuebunny/crossref_metadata_2025_split huggingface dataset:
One relative risk versus two odds ratios: implications for meta-analyses involving paired and unpaired binary data
Authors: Zou Guang Yong 
Published: February 2007

Background There are debates on whether the conditional odds ratio or marginal odds ratio should be used in meta-analysis involving both paired and unpaired binary data. Although statistically sound, both approaches result in overall odds ratios which are known to be less meaningful to consumers. Purpose To show that while two odds ratios can be calculated in a pair-matched study, there is only one relative risk for such design, and to discuss the implications for meta-analysis involving both paired and unpaired binary data. Methods Algebra and an example, along with standard software for implementing relative risk regression models. Results The choice of relative risk as the effect measure in pair-matched design not only simplifies analysis and interpretation for individual studies, but makes mata-analysis involving both paired and unpaired studies straightforward. Pooling marginal odds ratios in a meta-analysis of diabetic retinopathy treatment resulted in a summarized odds ratio of 2.25 (95% CI 1.83–2.75), compared with that of 2.44 (95% CI 1.95–3.04) from pooling conditional odds ratios. In contrast, summarizing relative risks resulted in an overall effect measure of 1.09 (95% CI 1.06–1.11), implying the treatment reduces visual deterioration rate by 9%. Conclusion Relative risk may be the first consideration in measuring effect for analyzing prospective studies with binary outcomes.
Using web-based screening to enhance efficiency of HMO clinical trial recruitment in women aged forty and older
Authors: Smith K Sabina , Eubanks Donna , Petrik Amanda , Stevens Victor J 
Published: February 2007

Background Screening potential participants for clinical trials can be labor-intensive, particularly when using long questionnaires administered by telephone. Purpose This report describes the development and use of an interactive recruitment website as a supplemental screening strategy for a study using telephone screening interviews. Methods Female HMO members, aged 40 and older, were recruited for a study testing dietary change interventions. Cohorts of potential participants were identified from electronic membership records every two to four weeks; they were sent a letter describing the study and then contacted by telephone. Those interested in the study were asked to complete a 27-question screening interview focused on dietary habits. After 14 cohorts of women were recruited by this method ( n = 4246), a recruitment website was added and an additional 12 cohorts ( n = 3000) were contacted. The modified recruitment letter for these later screening cohorts included the website address and a personal password for each woman. The website contained study information, and those who were interested could complete eligibility screening on-line. Results Proactive participant response (women actively seeking study participation/screening) to the recruitment mailing was 9.5% (95% confidence interval (CI), 8.6–10.4%) in the cohorts without the website option and 11.5% (CI, 10.4–12.7%) after addition of the website option ( P = 0.004). About half of women screened were ineligible for the study, a proportion that did not statistically differ by recruitment method. Limitations The study population was limited to middle-aged and older female members of a non-profit health plan, so the generalizability of these findings to other populations is unknown. The pre-post design used in this study does not control for possible temporal changes unrelated to the study methods. Conclusions The addition of the website screening option was associated with a relative 22% increase in recruitment combined with reduced staff time required for screening, thereby increasing screening efficiency. Web-based options for clinical trial recruitment and screening in targeted populations may increase response rates while also reducing staff time.
Innovative approaches to cohort retention in a community-based HIV/STI prevention trial for socially marginalized Peruvian young adults
Authors: Villacorta Victoria , Kegeles Susan , Galea Jerome , Konda Kelika A , Cuba José Pajuelo , Palacios Carlos F Cáceres , Coates Thomas J ,   NIMH Collaborative HIV/STD Prevention Trial Group
Published: February 2007

Background The conduct of longitudinal clinical trials must involve effective strategies to retain study participants in order to ensure internal validity, adequate statistical power and generalizability of results. Purpose In a large trial in Peru, we implemented various retention strategies to maintain high participation rates over time. Methods Novel participant retention strategies were used to follow highly marginalized populations for two years because traditional locator information, such as telephone numbers and official identification (eg, passport, driver's license, the local equivalent of a social security number) were often unreliable or unavailable. These strategies included detailed preliminary ethnographic research to identify the behaviours of key target groups, approaches to develop strong informal bonds between project staff and participants outside of study settings, and methods to enhance positive participant attitudes towards the study. Results The overall study retention rate after two years was 84%, even though only 26% of the study populations supplied complete locator information (telephone, address and the names of two friends). Limitations The retention strategies used were labour intensive and iterative, which could prove difficult to replicate. Conclusions The two-year retention rate in this study was sufficient to maintain required sample sizes. The methods used to maintain contact with the populations were labour intensive, low tech and adequate for these populations and could be used to retain study participants in other marginalized, urban, low-income areas.
Authority to Teach in Classical Anglicanism
Authors: Sixtus Bernhard 
Published: February 2007

AbstractAnglicanism currently finds itself embroiled in a variety of ‘controversies of Faith’ that individually and together threaten to split the Communion - and most of these concern questions of teaching and authority: who within Anglicanism has authority to teach what, and why? In this situation one naturally looks back on the tradition to seek how an understanding of the past may inform the present. The following paper does so by considering the concept of authority in the foundational period of ‘Anglicanism’, namely from the Thirty-nine Articles of the Church of England to the denominational ‘invention’ of Anglicanism after 1829. It discovers there three interrelated principles of an Anglican understanding of authority, which are briefly summarized after some remarks about how to use conclusions of papers such as this - and how not to.
Minimus: a fast, lightweight genome assembler
Authors: Sommer Daniel D , Delcher Arthur L , Salzberg Steven L , Pop Mihai 
Published: February 2007

Abstract

Background
Genome assemblers have grown very large and complex in response to the need for algorithms to handle the challenges of large whole-genome sequencing projects. Many of the most common uses of assemblers, however, are best served by a simpler type of assembler that requires fewer software components, uses less memory, and is far easier to install and run.

Results
We have developed the Minimus assembler to address these issues, and tested it on a range of assembly problems. We show that Minimus performs well on several small assembly tasks, including the assembly of viral genomes, individual genes, and BAC clones. In addition, we evaluate Minimus' performance in assembling bacterial genomes in order to assess its suitability as a component of a larger assembly pipeline. We show that, unlike other software currently used for these tasks, Minimus produces significantly fewer assembly errors, at the cost of generating a more fragmented assembly.

Conclusion
We find that for small genomes and other small assembly tasks, Minimus is faster and far more flexible than existing tools. Due to its small size and modular design Minimus is perfectly suited to be a component of complex assembly pipelines. Minimus is released as an open-source software project and the code is available as part of the AMOS project at Sourceforge.
Detection of the inferred interaction network in hepatocellular carcinoma from EHCO (E ncyclopedia of H epatocellular C arcinoma genes O nline)
Authors: Hsu Chun-Nan , Lai Jin-Mei , Liu Chia-Hung , Tseng Huei-Hun , Lin Chih-Yun , Lin Kuan-Ting , Yeh Hsu-Hua , Sung Ting-Yi , Hsu Wen-Lian , Su Li-Jen , Lee Sheng-An , Chen Chang-Han , Lee Gen-Cher , Lee DT , Shiue Yow-Ling , Yeh Chang-Wei , Chang Chao-Hui , Kao Cheng-Yan , Huang Chi-Ying F 
Published: February 2007

AbstractBackgroundThe significant advances in microarray and proteomics analyses have resulted in an exponential increase in potential new targets and have promised to shed light on the identification of disease markers and cellular pathways. We aim to collect and decipher the HCC-related genes at the systems level.ResultsHere, we build an integrative platform, theEncyclopedia ofHepatocellularCarcinoma genesOnline, dubbed EHCOhttp://ehco.iis.sinica.edu.tw, to systematically collect, organize and compare the pileup of unsorted HCC-related studies by using natural language processing and softbots. Among the eight gene set collections, ranging across PubMed, SAGE, microarray, and proteomics data, there are 2,906 genes in total; however, more than 77% genes are only included once, suggesting that tremendous efforts need to be exerted to characterize the relationship between HCC and these genes. Of these HCC inventories, protein binding represents the largest proportion (~25%) from Gene Ontology analysis. In fact, many differentially expressed gene sets in EHCO could form interaction networks (e.g. HBV-associated HCC network) by using available human protein-protein interaction datasets. To further highlight the potential new targets in the inferred network from EHCO, we combine comparative genomics and interactomics approaches to analyze 120 evolutionary conserved and overexpressed genes in HCC. 47 out of 120 queries can form a highly interactive network with 18 queries serving as hubs.ConclusionThis architectural map may represent the first step toward the attempt to decipher the hepatocarcinogenesis at the systems level. Targeting hubs and/or disruption of the network formation might reveal novel strategy for HCC treatment.
Full Length Bid is sufficient to induce apoptosis of cultured rat hippocampal neurons
Authors: König Hans-Georg , Rehm Markus , Gudorf Daniel , Krajewski Stan , Gross Atan , Ward Manus W , Prehn Jochen HM 
Published: February 2007

AbstractBackgroundBcl-2 homology domain (BH) 3-only proteins are pro-apoptotic proteins of the Bcl-2 family that couple stress signals to the mitochondrial cell death pathways. The BH3-only protein Bid can be activated in response to death receptor activation via caspase 8-mediated cleavage into a truncated protein (tBid), which subsequently translocates to mitochondria and induces the release of cytochrome-C. Using a single-cell imaging approach of Bid cleavage and translocation during apoptosis, we have recently demonstrated that, in contrast to death receptor-induced apoptosis, caspase-independent excitotoxic apoptosis involves a translocation of full length Bid (FL-Bid) from the cytosol to mitochondria. We induced a delayed excitotoxic cell death in cultured rat hippocampal neurons by a 5-min exposure to the glutamate receptor agonist N-methyl-D-aspartate (NMDA; 300 μM).ResultsWestern blot experiments confirmed a translocation of FL-Bid to the mitochondria during excitotoxic apoptosis that was associated with the release of cytochrome-C from mitochondria. These results were confirmed by immunofluorescence analysis of Bid translocation during excitotoxic cell death using an antibody raised against the amino acids 1–58 of mouse Bid that is not able to detect tBid. Finally, inducible overexpression of FL-Bid or a Bid mutant that can not be cleaved by caspase-8 was sufficient to induce apoptosis in the hippocampal neuron cultures.ConclusionOur data suggest that translocation of FL-Bid is sufficient for the activation of mitochondrial cell death pathways in response to glutamate receptor overactivation.
The evolutionary history of Cytochrome P450 genes in four filamentous Ascomycetes
Authors: Deng Jixin , Carbone Ignazio , Dean Ralph A 
Published: February 2007

Abstract

Background
The Cytochrome P450 system is important in fungal evolution for adapting to novel ecological niches. To elucidate the evolutionary process of cytochrome P450 genes in fungi with different life styles, we studied the patterns of gene gains and losses in the genomes of four filamentous Ascomycetes, including two saprotrophs (Aspergillus nidulans (AN) and Neurospora crassa (NC)) and two plant pathogens (Fusarium graminearum (FG) and Magnaporthe grisea (MG)).

Results
A total of 376 P450 genes were assigned to 168 families according to standard nomenclature. On average, only 1 to 2 genes per family were in each genome. To resolve conflicting results between different clustering analyses and standard family designation, a higher order relationship was formulated. 376 genes were clustered into 115 clans. Subsequently a novel approach based on parsimony was developed to build the evolutionary models. Based on these analyses, a core of 30 distinct clans of P450s was defined. The core clans experienced contraction in all four fungal lineages while new clans expanded in all with exception of NC. MG experienced more genes and clans gains compared to the other fungi. Parsimonious analyses unanimously supported one species topology for the four fungi.

Conclusion
The four studied fungi exhibit unprecedented diversity in their P450omes in terms of coding sequence, intron-exon structures and genome locations, suggesting a complicated evolutionary history of P450s in filamentous Ascomycetes. Clan classification and a novel strategy were developed to study evolutionary history. Contraction of core clans and expansion of novel clans were identified. The exception was the NC lineage, which exhibited pure P450 gene loss.
No association between the PREP gene and lithium responsive bipolar disorder
Authors: Mamdani Firoza , Sequeira Adolfo , Alda Martin , Grof Paul , Rouleau Guy , Turecki Gustavo 
Published: February 2007

Abstract

Background
Bipolar disorder (BD) is a major psychiatric condition that commonly requires prophylactic and episodic treatment. Lithium (Li) has been used for over 40 years now as an effective prophylactic agent. Response to Li treatment seems to be, at least in part, genetically determined. Although we ignore how Li specifically prevents mood episodes, it has previously been suggested that Li exerts an effect on the phosphoinositide pathway, and more recently, it has been proposed that Li may modulate prolyl endopeptidase (PREP).

Methods
In this study we carried out an association study looking at the PREP gene, located on ch 6q22. Five intronic single nucleotide polymorphisms (SNP), three coding SNPs and one SNP in the 5' UTR were investigated for their frequency in a BD sample of 180 excellent Li responders, 69 Li nonresponders and 126 controls. Genotyping was carried out using the SNaPshot reaction from Applied Biosystems, which is a modified fluorescent single base pair extension procedure.

Results
Following correction for multiple testing, no significant genotypic, allelic or estimated haplotypic differences were found between responders and nonresponders or between BD patients and controls.

Conclusion

PREP is an interesting candidate gene to investigate in genetic studies of BD, but our findings do not support the hypothesis that genetic variation in this gene plays a major role in the etiology of BD or Li response.
The links between health-related behaviors and life satisfaction in elderly individuals who prefer institutional living
Authors: Inal Serap , Subasi Feryal , Ay Serap M , Hayran Osman 
Published: February 2007

Abstract

Background
Life satisfaction among residents of institutions is becoming an important issue in a rapidly aging population. The aim of this cross-sectional study was to investigate the links between life satisfaction and health-related behaviors amongst functionally independent elderly people who prefer institutional living in İstanbul, Turkey.

Methods
The socio-demographic characteristics, health-related behaviors, leisure-time activities and fall histories of 133 residents of an institution in Istanbul were assessed by a structured questionnaire during face-to-face interviews. A validated life-satisfaction index questionnaire (LSI-A) was completed.

Results
The mean age of the study group was 73.9 ± 8.0 (range 60–90 years). Within the group, 22.6% had never married and 14.3% had university degrees. The majority (71.4%) were in the low income bracket. The overall mean LSI-A score was 20.3 ± 5.9. Participants who declared moderate/high income levels had a significantly higher mean LSI-A score than those in the low-income bracket (p = 0.009). Multivariate analysis of the data suggested that leisure-time activities and participation in regular physical activities are significant predictors of LSI-A scores (R2: 0.112; p = 0.005 and p = 0.02, respectively).

Conclusion
The findings imply that regular physical activity and leisure-time activities are significantly related to life satisfaction among residents in institutions. Participation in physical activity and leisure-time activity programs may help to improve the life satisfaction of elderly people living in institutions.
Evaluation of the reach and impact of the 100% Jeune youth social marketing program in Cameroon: findings from three cross-sectional surveys
Authors: Plautz Andrea , Meekers Dominique 
Published: February 2007

Abstract
Background
The 100% Jeune youth social marketing program in Cameroon aims to address the high STI/HIV prevalence rates and the high levels of unwanted pregnancy. This study evaluates the 100% Jeune program, analyzing its reach and impact on condom use, level of sexual activity, and predictors of condom use.

Methods
This analysis uses data from three waves of the Cameroon Adolescent Reproductive Health Survey, implemented at 18-month intervals between 2000 and 2003. The sample is restricted to unmarried youth aged 15–24; sample sizes are 1,956 youth in 2000, 3,237 in 2002, and 3,370 in 2003. Logistic regression analyses determine trends in reproductive health behavior and their predictors, as well as estimate the effect of program exposure on these variables. All regression analyses control for differences in sample characteristics.

Results
A comparison of trends over the 36-month study period shows that substantial positive changes occurred among youth. Results of dose response analyses indicate that some of these positive changes in condom use and predictors of use can be attributed to the 100% Jeune youth social marketing program. The program contributed to substantial increases in condom use, including consistent use with regular partners among youth of both sexes. Among males, it also contributed to consistent use with casual partners. While condom use increased with both regular and casual partners, levels of use are higher with the latter. Observed secular trends indicate that factors besides the 100% Jeune program also contributed to the observed improvements. Despite efforts to promote abstinence, the 100% Jeune program had no effect on levels of sexual activity or number of sexual partners. Likewise, there is no evidence that reproductive health programs for youth lead to increased sexual activity.

Conclusion
Results show that 100% Jeune successfully used a variety of mass media and interpersonal communication channels to reach a high proportion of youth throughout the intervention period. In a context in which a variety of governmental and nongovernmental partners are increasing youth-focused reproductive health programming, the 100% Jeune program reached a higher proportion of youth than did other programs. Collective efforts of multiple organizations over time can lead to improvements in adolescent reproductive health. Resources should be allocated to identify and understand predictors of abstinence and partner reduction to inform future programming decisions.
The effects of DNA methylation and histone deacetylase inhibitors on human papillomavirus early gene expression in cervical cancer, an in vitro and clinical study
Authors: de la Cruz-Hernández Erick , Pérez-Cárdenas Enrique , Contreras-Paredes Adriana , Cantú David , Mohar Alejandro , Lizano Marcela , Dueñas-González Alfonso 
Published: February 2007

Abstract

Background
The methylation status at the human papilloma virus (HPV) genome found in pre-invasive and invasive cervical lesions suggests that neoplastic transformation can be suppressed by gene hypermethylation, whereas hypomethylation accompanies or causes cancer progression; hence, epigenetic therapy aimed at reactivating cellular suppressor-gene expression has the potential to act as a tumor promoter by enhancing HPV oncoprotein expression in HPV-related malignancies. The objective of this study was to determine the influence of hydralazine and valproate on HPV oncogene expression in cervical cancer cell lines and the primary tumors of patients undergoing treatment with hydralazine and valproate.

Results
Overall, hydralazine and valproate either alone or combined exerted a growth inhibitory effect on cervical cancer cell lines. A cell line-specific up-regulating effect was observed on E6/E7 gene expression, which in general correlated with DNA hypomethylation and histone acetylation at the long control region (LCR). Nonetheless, E6/E7 expression was unchanged or decreased in the majority of patients with cervical cancer treated with hydralazine, valproate, or both. In some cervical cancer cell lines, these drugs led to increased transcription of p53, and increased its stabilization due to acetylation at lysines 273 and 282, which allowed a higher bax-protein transactivating effect.

Conclusion
The results of this study demonstrate that hydralazine and valproate can be safely administered to HPV-related malignancies such as cervical cancer because they do not increase viral oncoprotein expression. Most importantly, the antitumor effect of hydralazine and valproate in cervical cancer may at least partially depend on an up-regulating effect on p53 gene and on the valproate-induced hyperacetylation of p53 protein, protecting it from degradation by E6.