bluuebunny/crossref_metadata_2025 huggingface dataset:
Spatial normalization of array-CGH data
Authors: Neuvial Pierre , Hupé Philippe , Brito Isabel , Liva Stéphane , Manié Élodie , Brennetot Caroline , Radvanyi François , Aurias Alain , Barillot Emmanuel
Published: May 2006

Background

Array-based comparative genomic hybridization (array-CGH) is a recently developed technique for analyzing changes in DNA copy number. As in all microarray analyses, normalization is required to correct for experimental artifacts while preserving the true biological signal. We investigated various sources of systematic variation in array-CGH data and identified two distinct types of spatial effect of no biological relevance as the predominant experimental artifacts: continuous spatial gradients and local spatial bias. Local spatial bias affects a large proportion of arrays, and has not previously been considered in array-CGH experiments.

Results

We show that existing normalization techniques do not correct these spatial effects properly. We therefore developed an automatic method for the spatial normalization of array-CGH data. This method makes it possible to delineate and to eliminate and/or correct areas affected by spatial bias. It is based on the combination of a spatial segmentation algorithm called NEM (Neighborhood Expectation Maximization) and spatial trend estimation. We defined quality criteria for array-CGH data, demonstrating significant improvements in data quality with our method for three data sets coming from two different platforms (198, 175 and 26 BAC-arrays).

Conclusion

We have designed an automatic algorithm for the spatial normalization of BAC CGH-array data, preventing the misinterpretation of experimental artifacts as biologically relevant outliers in the genomic profile. This algorithm is implemented in the R package MANOR (Micro-Array NORmalization), which is described at http://bioinfo.curie.fr/projects/manor and available from the Bioconductor site http://www.bioconductor.org. It can also be tested on the CAPweb bioinformatics platform at http://bioinfo.curie.fr/CAPweb.
A jumping profile Hidden Markov Model and applications to recombination sites in HIV and HCV genomes
Authors: Schultz Anne-Kathrin , Zhang Ming , Leitner Thomas , Kuiken Carla , Korber Bette , Morgenstern Burkhard , Stanke Mario
Published: May 2006

Background

Jumping alignments have recently been proposed as a strategy to search a given multiple sequence alignment A against a database. Instead of comparing a database sequence S to the multiple alignment or profile as a whole, S is compared and aligned to individual sequences from A. Within this alignment, S can jump between different sequences from A, so different parts of S can be aligned to different sequences from the input multiple alignment. This approach is particularly useful for dealing with recombination events.

Results

We developed a jumping profile Hidden Markov Model (jpHMM), a probabilistic generalization of the jumping-alignment approach. Given a partition of the aligned input sequence family into known sequence subtypes, our model can jump between states corresponding to these different subtypes, depending on which subtype is locally most similar to a database sequence. Jumps between different subtypes are indicative of intersubtype recombinations. We applied our method to a large set of genome sequences from human immunodeficiency virus (HIV) and hepatitis C virus (HCV) as well as to simulated recombined genome sequences.

Conclusion

Our results demonstrate that jumps in our jumping profile HMM often correspond to recombination breakpoints; our approach can therefore be used to detect recombinations in genomic sequences. The recombination breakpoints identified by jpHMM were found to be significantly more accurate than breakpoints defined by traditional methods based on comparing single representative sequences.
Phylogeny based discovery of regulatory elements
Authors: Gertz Jason , Fay Justin C , Cohen Barak A
Published: May 2006

Background

Algorithms that locate evolutionarily conserved sequences have become powerful tools for finding functional DNA elements, including transcription factor binding sites; however, most methods do not take advantage of an explicit model for the constrained evolution of functional DNA sequences.

Results

We developed a probabilistic framework that combines an HKY85 model, which assigns probabilities to different base substitutions between species, and weight matrix models of transcription factor binding sites, which describe the probabilities of observing particular nucleotides at specific positions in the binding site. The method incorporates the phylogenies of the species under consideration and takes into account the position specific variation of transcription factor binding sites. Using our framework we assessed the suitability of alignments of genomic sequences from commonly used species as substrates for comparative genomic approaches to regulatory motif finding. We then applied this technique to Saccharomyces cerevisiae and related species by examining all possible six base pair DNA sequences (hexamers) and identifying sequences that are conserved in a significant number of promoters. By combining similar conserved hexamers we reconstructed known cis-regulatory motifs and made predictions of previously unidentified motifs. We tested one prediction experimentally, finding it to be a regulatory element involved in the transcriptional response to glucose.

Conclusion

The experimental validation of a regulatory element prediction missed by other large-scale motif finding studies demonstrates that our approach is a useful addition to the current suite of tools for finding regulatory motifs.
Cadherin2 (N-cadherin) plays an essential role in zebrafish cardiovascular development
Authors: Bagatto Brian , Francl Jessie , Liu Bei , Liu Qin
Published: May 2006

Background

Cadherins are cell surface adhesion molecules that play important roles in development of vertebrate tissues and organs. We studied cadherin2 expression in developing zebrafish heart using in situ hybridization and immunocytochemical methods, and we found that cadherin2 was strongly expressed by the myocardium of the embryonic zebrafish. To gain insight into cadherin2 role in the formation and function of the heart, we analyzed cardiac differentiation and performance in a cadherin2 mutant, glass onion (glo).

Results

We found that the cadherin2 mutant had enlarged pericardial cavity, disorganized atrium and ventricle, and reduced expression of a ventricular specific marker vmhc. Individual myocardiocytes in the glo mutant embryos became round shaped and loosely aggregated. In vivo measurements of cardiac performance revealed that the mutant heart had significantly reduced heart rate, stroke volume and cardiac output compared to control embryos. Formation of the embryonic vascular system in the glo mutants was also affected.

Conclusion

Our results suggest that cadherin2 plays an essential role in zebrafish cardiovascular development. Although the exact mechanisms remain unknown as to the formation of the enlarged pericardium and reduced peripheral blood flow, it is clear that myocardiocyte differentiation and physiological cardiovascular performance is impaired when cadherin2 function is disrupted.
Phenotype-genotype association grid: a convenient method for summarizing multiple association analyses
Authors: Levy Daniel , DePalma Steven R , Benjamin Emelia J , O'Donnell Christopher J , Parise Helen , Hirschhorn Joel N , Vasan Ramachandran S , Izumo Seigo , Larson Martin G
Published: May 2006

Background

High-throughput genotyping generates vast amounts of data for analysis; results can be difficult to summarize succinctly. A single project may involve genotyping many genes with multiple variants per gene and analyzing each variant in relation to numerous phenotypes, using several genetic models and population subgroups. Hundreds of statistical tests may be performed for a single SNP, thereby complicating interpretation of results and inhibiting identification of patterns of association.

Results

To facilitate visual display and summary of large numbers of association tests of genetic loci with multiple phenotypes, we developed a Phenotype-Genotype Association (PGA) grid display. A database-backed web server was used to create PGA grids from phenotypic and genotypic data (sample sizes, means and standard errors, P-value for association). HTML pages were generated using Tcl scripts on an AOLserver platform, using an Oracle database, and the ArsDigita Community System web toolkit. The grids are interactive and permit display of summary data for individual cells by a mouse click (i.e. least squares means for a given SNP and phenotype, specified genetic model and study sample). PGA grids can be used to visually summarize results of individual SNP associations, gene-environment associations, or haplotype associations.

Conclusion

The PGA grid, which permits interactive exploration of large numbers of association test results, can serve as an easily adapted common and useful display format for large-scale genetic studies. Doing so would reduce the problem of publication bias, and would simplify the task of summarizing large-scale association studies.
Widespread ectopic expression of olfactory receptor genes
Authors: Feldmesser Ester , Olender Tsviya , Khen Miriam , Yanai Itai , Ophir Ron , Lancet Doron
Published: May 2006

Background

Olfactory receptors (ORs) are the largest gene family in the human genome. Although they are expected to be expressed specifically in olfactory tissues, some ectopic expression has been reported, with special emphasis on sperm and testis. The present study systematically explores the expression patterns of OR genes in a large number of tissues and assesses the potential functional implication of such ectopic expression.

Results

We analyzed the expression of hundreds of human and mouse OR transcripts, via EST and microarray data, in several dozens of human and mouse tissues. Different tissues had specific, relatively small OR gene subsets which had particularly high expression levels. In testis, average expression was not particularly high, and very few highly expressed genes were found, none corresponding to ORs previously implicated in sperm chemotaxis. Higher expression levels were more common for genes with a non-OR genomic neighbor. Importantly, no correlation in expression levels was detected for human-mouse orthologous pairs. Also, no significant difference in expression levels was seen between intact and pseudogenized ORs, except for the pseudogenes of subfamily 7E which has undergone a human-specific expansion.

Conclusion

The OR superfamily as a whole, show widespread, locus-dependent and heterogeneous expression, in agreement with a neutral or near neutral evolutionary model for transcription control. These results cannot reject the possibility that small OR subsets might play functional roles in different tissues, however considerable care should be exerted when offering a functional interpretation for ectopic OR expression based only on transcription information.
The mitochondrial lineage U8a reveals a Paleolithic settlement in the Basque country
Authors: González Ana M , García Oscar , Larruga José M , Cabrera Vicente M
Published: May 2006

Background

It is customary, in population genetics studies, to consider Basques as the direct descendants of the Paleolithic Europeans. However, until now there has been no irrefutable genetic proof to support this supposition. Even studies based on mitochondrial DNA (mtDNA), an ideal molecule for constructing datable maternal genealogies, have failed to achieve this. It could be that incoming gene flow has replaced the Basque ancient lineages but it could also be that these lineages have not been detected due to a lack of resolution of the Basque mtDNA genealogies. To assess this possibility we analyzed here the mtDNA of a large sample of autochthonous Basques using mtDNA genomic sequencing for those lineages that could not be unequivocally classified by diagnostic RFLP analysis and control region (HVSI and HVSII) sequencing.

Results

We show that Basques have the most ancestral phylogeny in Europe for the rare mitochondrial subhaplogroup U8a. Divergence times situate the Basque origin of this lineage in the Upper Palaeolithic. Most probably, their primitive founders came from West Asia. The lack of U8a lineages in Africa points to an European and not a North African route of entrance. Phylogeographic analysis suggest that U8a had two expansion periods in Europe, the first, from a south-western area including the Iberian peninsula and Mediterranean France before 30,000 years ago, and the second, from Central Europe around 15,000–10,000 years ago.

Conclusion

It has been demonstrated, for the first time, that Basques show the oldest lineages in Europe for subhaplogroup U8a. Coalescence times for these lineages suggest their presence in the Basque country since the Upper Paleolithic. The European U8 phylogeography is congruent with the supposition that Basques could have participated in demographic re-expansions to repopulate central Europe in the last interglacial periods.
Texture discrimination and multi-unit recording in the rat vibrissal nerve
Authors: Albarracín Ana L , Farfán Fernando D , Felice Carmelo J , Décima Emilio E
Published: May 2006

Background

Rats distinguish objects differing in surface texture by actively moving their vibrissae. In this paper we characterized some aspects of texture sensing in anesthetized rats during active touch. We analyzed the multifiber discharge from a deep vibrissal nerve when the vibrissa sweeps materials (wood, metal, acrylic, sandpaper) having different textures. We polished these surfaces with sandpaper (P1000) to obtain close degrees of roughness and we induced vibrissal movement with two-branch facial nerve stimulation. We also consider the change in pressure against the vibrissa as a way to improve the tactile information acquisition. The signals were compared with a reference signal (control) – vibrissa sweeping the air – and were analyzed with the Root Mean Square (RMS) and the Power Spectrum Density (PSD).

Results

We extracted the information about texture discrimination hidden in the population activity of one vibrissa innervation, using the RMS values and the PSD. The pressure level 3 produced the best differentiation for RMS values and it could represent the "optimum" vibrissal pressure for texture discrimination. The frequency analysis (PSD) provided information only at low-pressure levels and showed that the differences are not related to the roughness of the materials but could be related to other texture parameters.

Conclusion

Our results suggest that the physical properties of different materials could be transduced by the trigeminal sensory system of rats, as are shown by amplitude and frequency changes. Likewise, varying the pressure could represent a behavioral strategy that improves the information acquisition for texture discrimination.
Association study of genetic variants of pro-inflammatory chemokine and cytokine genes in systemic lupus erythematosus
Authors: Sánchez Elena , Sabio José M , Callejas José L , de Ramón Enrique , Garcia-Portales Rosa , García-Hernández Francisco J , Jiménez-Alonso Juan , González-Escribano Ma Francisca , Martín Javier , Koeleman Bobby P
Published: May 2006

Background

Several lines of evidence suggest that chemokines and cytokines play an important role in the inflammatory development and progression of systemic lupus erythematosus. The aim of this study was to evaluate the relevance of functional genetic variations of RANTES, IL-8, IL-1α, and MCP-1 for systemic lupus erythematosus.

Methods

The study was conducted on 500 SLE patients and 481 ethnically matched healthy controls. Genotyping of polymorphisms in the RANTES, IL-8, IL-1α, and MCP-1 genes were performed using a real-time polymerase chain reaction (PCR) system with pre-developed TaqMan allelic discrimination assay.

Results

No significant differences between SLE patients and healthy controls were observed when comparing genotype, allele or haplotype frequencies of the RANTES, IL-8, IL-1α, and MCP-1 polymorphisms. In addition, no evidence for association with clinical sub-features of SLE was found.

Conclusion

These results suggest that the tested functional variation of RANTES, IL-8, IL-1α, and MCP-1 genes do not confer a relevant role in the susceptibility or severity of SLE in the Spanish population.
Identification of novel functional sequence variants in the gene for peptidase inhibitor 3
Authors: Chowdhury Mahboob A , Kuivaniemi Helena , Romero Roberto , Edwin Samuel , Chaiworapongsa Tinnakorn , Tromp Gerard
Published: May 2006

Background

Peptidase inhibitor 3 (PI3) inhibits neutrophil elastase and proteinase-3, and has a potential role in skin and lung diseases as well as in cancer. Genome-wide expression profiling of chorioamniotic membranes revealed decreased expression of PI3 in women with preterm premature rupture of membranes. To elucidate the molecular mechanisms contributing to the decreased expression in amniotic membranes, the PI3 gene was searched for sequence variations and the functional significance of the identified promoter variants was studied.

Methods

Single nucleotide polymorphisms (SNPs) were identified by direct sequencing of PCR products spanning a region from 1,173 bp upstream to 1,266 bp downstream of the translation start site. Fourteen SNPs were genotyped from 112 and nine SNPs from 24 unrelated individuals. Putative transcription factor binding sites as detected by in silico search were verified by electrophoretic mobility shift assay (EMSA) using nuclear extract from Hela and amnion cell nuclear extract. Deviation from Hardy-Weinberg equilibrium (HWE) was tested by χ2 goodness-of-fit test. Haplotypes were estimated using expectation maximization (EM) algorithm.

Results

Twenty-three sequence variations were identified by direct sequencing of polymerase chain reaction (PCR) products covering 2,439 nt of the PI3 gene (-1,173 nt of promoter sequences and all three exons). Analysis of 112 unrelated individuals showed that 20 variants had minor allele frequencies (MAF) ranging from 0.02 to 0.46 representing "true polymorphisms", while three had MAF ≤ 0.01. Eleven variants were in the promoter region; several putative transcription factor binding sites were found at these sites by database searches. Differential binding of transcription factors was demonstrated at two polymorphic sites by electrophoretic mobility shift assays, both in amniotic and HeLa cell nuclear extracts. Differential binding of the transcription factor GATA1 at -689C>G site was confirmed by a supershift.

Conclusion

The promoter sequences of PI3 have a high degree of variability. Functional promoter variants provide a possible mechanism for explaining the differences in PI3 mRNA expression levels in the chorioamniotic membranes, and are also likely to be useful in elucidating the role of PI3 in other diseases.
Stigma in response to mental disorders: a comparison of Australia and Japan
Authors: Griffiths Kathleen M , Nakane Yoshibumi , Christensen Helen , Yoshioka Kumiko , Jorm Anthony F , Nakane Hideyuki
Published: May 2006

Background

There are few national or cross-cultural studies of the stigma associated with mental disorders. Australia and Japan have different systems of psychiatric health care, and distinct differences in cultural values, but enjoy similar standards of living. This study seeks to compare the nature and extent of stigma among the public in the two countries.

Methods

A household survey of the public was conducted in each country using similar methodologies. The Australian study comprised a national survey of 3998 adults aged over 18 years. The Japanese survey involved 2000 adults aged 20 to 69 from 25 regional sites distributed across the country. Interviewees reported their personal attitudes (personal stigma, social distance) and perceptions of the attitudes of others (perceived stigma, perceived discrimination) in the community with respect to four case vignettes. These vignettes described a person with: depression; depression with suicidal ideation; early schizophrenia; and chronic schizophrenia.

Results

Personal stigma and social distance were typically greater among the Japanese than the Australian public whereas the reverse was true with respect to the perception of the attitudes and discriminatory behaviour of others. In both countries, personal stigma was significantly greater than perceived stigma. The public in both countries showed evidence of greater social distance, greater personal stigma and greater perceived stigma for schizophrenia (particularly in its chronic form) than for depression. There was little evidence of a difference in stigma for depression with and without suicide for either country. However, social distance was greater for chronic compared to early schizophrenia for the Australian public.

Conclusion

Stigmatising attitudes were common in both countries, but negative attitudes were greater among the Japanese than the Australian public. The results suggest that there is a need to implement national public awareness interventions tailored to the needs of each country. The current results provide a baseline for future tracking of national stigma levels in each country.
Avoidable mortality across Canada from 1975 to 1999
Authors: James Paul D , Manuel Doug G , Mao Yang
Published: May 2006

Background

The concept of 'avoidable' mortality (AM) has been proposed as a performance measure of health care systems. In this study we examined mortality in five geographic regions of Canada from 1975 to 1999 for previously defined avoidable disease groups that are amenable to medical care and public health. These trends were compared to mortality from other causes.

Methods

National and regional age-standardized mortality rates for ages less than 65 years were estimated for avoidable and other causes of death for consecutive periods (1975–1979, 1980–1985, 1985–1989, 1990–1994, and 1995–1999). The proportion of all-cause mortality attributable to avoidable causes was also determined.

Results

From 1975–1979 to 1995–1999, the AM decrease (46.9%) was more pronounced compared to mortality from other causes (24.9%). There were persistent regional AM differences, with consistently lower AM in Ontario and British Columbia compared to the Atlantic, Quebec, and Prairies regions. This trend was not apparent when mortality from other causes was examined. Injuries, ischaemic heart disease, and lung cancer strongly influenced the overall AM trends.

Conclusion

The regional differences in mortality for ages less than 65 years was attributable to causes of death amenable to medical care and public health, especially from causes responsive to public health.
Patterns of smoking behavior among physicians in Yerevan, Armenia
Authors: Perrin Paul C , Merrill Ray M , Lindsay Gordon B
Published: May 2006

Background

Physicians can play an important role in smoking prevention and control. This study will identify smoking prevalence among physicians in Yerevan, Armenia. It will also explore how the smoking behaviors of physicians, their perceived ability to influence patient smoking behavior, and their knowledge about health outcomes related to smoking influence their interaction with patients.

Methods

A cross-sectional, self-administered, anonymous survey was conducted in July, 2004, among 12 healthcare facilities in Yerevan. Analyses are based on responses from 240 physicians, representing a 70% response rate.

Results

The percentage of current smokers was significantly higher in men than women (48.5% vs. 12.8% regular and 6.8% vs. 4.5% occasional). Among current smokers, 52.7% of men compared with 13.0% of women had previously smoked in the presence of patients. Only 35.3% felt well prepared to assist patients to quit smoking. Physicians who smoke are less likely to ask their patients about their smoking behavior or believe their example is likely to influence their patients. Level of perceived preparedness to assist patients to quit smoking was positively associated with knowledge about known health risks associated with smoking.

Conclusion

Smoking prevalence is high among physicians in the 12 healthcare facilities in Yerevan, and a large percentage of physician smoke in the presence of their patients. Physician smoking behavior and knowledge of smoking related health outcomes in Yerevan influences whether they counsel patients regarding smoking.
Construction, purification, and characterization of a chimeric TH1 antagonist
Authors: Bello-Rivero Iraldo , Torrez-Ruiz Yeny , Blanco-Garcés Elizabeth , Pentón-Rol Giselle , Fernández-Batista Osmani , Javier-González Luís , Gerónimo-Perez Haydee , López-Saura Pedro
Published: May 2006

Background

TH1 immune response antagonism is a desirable approach to mitigate some autoimmune and inflammatory reactions during the course of several diseases where IL-2 and IFN-γ are two central players. Therefore, the neutralization of both cytokines could provide beneficial effects in patients suffering from autoimmune or inflammatory illnesses.

Results

A chimeric antagonist that can antagonize the action of TH1 immunity mediators, IFN-γ and IL-2, was designed, engineered, expressed inE. coli, purified and evaluated for its in vitro biological activities. The TH1 antagonist molecule consists of the extracellular region for the human IFNγ receptor chain 1 fused by a four-aminoacid linker peptide to human 60 N-terminal aminoacid residues of IL-2. The corresponding gene fragments were isolated by RT-PCR and cloned in the pTPV-1 vector.E. coli(W3110 strain) was transformed with this vector. The chimeric protein was expressed at high level as inclusion bodies. The protein was partially purified by pelleting and washing. It was then solubilized with strong denaturant and finally refolded by gel filtration. In vitro biological activity of chimera was demonstrated by inhibition of IFN-γ-dependent HLA-DR expression in Colo 205 cells, inhibition of IFN-γ antiproliferative effect on HEp-2 cells, and by a bidirectional effect in assays for IL-2 T-cell dependent proliferation: agonism in the absence versus inhibition in the presence of IL-2.

Conclusion

TH1 antagonist is a chimeric protein that inhibits the in vitro biological activities of human IFN-γ, and is a partial agonist/antagonist of human IL-2. With these attributes, the chimera has the potential to offer a new opportunity for the treatment of autoimmune and inflammatory diseases.
Use of complementary and alternative medicine in Germany – a survey of patients with inflammatory bowel disease
Authors: Joos Stefanie , Rosemann Thomas , Szecsenyi Joachim , Hahn Eckhart G , Willich Stefan N , Brinkhaus Benno
Published: May 2006

Background

Previous studies have suggested an increasing use of complementary and alternative medicine (CAM) in patients with inflammatory bowel disease (IBD). The aim of our study was to evaluate the use of CAM in German patients with IBD.

Methods

A questionnaire was offered to IBD patients participating in patient workshops which were organized by a self-help association, the German Crohn's and Colitis Association. The self-administered questionnaire included demographic and disease-related data as well as items analysing the extent of CAM use and satisfaction with CAM treatment. Seven commonly used CAM methods were predetermined on the questionnaire.

Results

413 questionnaires were completed and included in the analysis (n = 153 male, n = 260 female; n = 246 Crohn's disease, n = 164 ulcerative colitis). 52 % of the patients reported CAM use in the present or past. In detail, homeopathy (55%), probiotics (43%), classical naturopathy (38%), Boswellia serrata extracts (36%) and acupuncture/Traditional Chinese Medicine (TCM) (33%) were the most frequently used CAM methods. Patients using probiotics, acupuncture and Boswellia serrata extracts (incense) reported more positive therapeutic effects than others. Within the statistical analysis no significant predictors for CAM use were found. 77% of the patients felt insufficiently informed about CAM.

Conclusion

The use of CAM in IBD patients is very common in Germany, although a large proportion of patients felt that information about CAM is not sufficient. However, to provide an evidence-based approach more research in this field is desperately needed. Therefore, physicians should increasingly inform IBD patients about benefits and limitations of CAM treatment.
Vibratory stimulation increase the electro-cutaneous sensory detection and pain thresholds in women but not in men
Authors: Dahlin Lisbeth , Lund Irene , Lundeberg Thomas , Molander Carl
Published: May 2006

Background

Vibratory stimulation is a potential method for the treatment of pain.

Methods

The effect of vibration on the forearm on detection (DT) and pain thresholds (PT) induced by electro-cutaneous stimulation were investigated in healthy male and female volunteers.

Results

Women have lower baseline detection and pain thresholds as compared to men. Furthermore, women but not men report increased detection and pain thresholds after vibratory stimulation.

Conclusion

Our findings indicate the potential usefulness of vibratory stimulation for pain treatment, and that gender differences should be considered in future evaluation of the method.
Variation in recruitment across sites in a consent-based clinical data registry: lessons from the Canadian Stroke Network
Authors: Willison Donald J , Kapral Moira K , Peladeau Pierrot , Richards Janice A , Fang Jiming , Silver Frank L
Published: May 2006

Background

In earlier work, we found important selection biases when we tried to obtain consent for participation in a national stroke registry. Recognizing that not all registries will be exempt from requiring consent for participation, we examine here in greater depth the reasons for the poor accrual of patients from a systems perspective with a view to obtaining as representative sample as possible.

Methods

We determined the percent of eligible patients who were approached to participate and, among those approached, the percent who actually consented to participate. In addition we examined the reasons why people were not approached or did not consent and the variation across sites in the percent of patients approached and consented. We also considered site variation in restrictions on the accrual and data collection process imposed by either the local research ethics board or the hospital.

Results

Seventy percent of stroke patients were approached, with wide variations in approach rates across sites (from: 41% to 86%), and considerable inter-site variation in hospital policies governing patient accrual. Chief reasons for not approaching were discharge or death before being approached for consent. Seventeen percent of those approached refused to participate (range: 5% to 75%). Finally, 11% of those approached did not participate due to language or communication difficulties.

Conclusion

We found wide variation in approach and agree rates across sites that were accounted for, in part, by different approaches to accrual and idiosyncratic policies of the hospitals. This wide variation in approach and agree rates raises important challenges for research ethics boards and data protection authorities in determining when to waive consent requirements, when to press for increased quality control, when to permit local adaptation of the consent process, and when to permit alternatives to individual express consent. We offer several suggestions for those registries that require consent for participation.
Improvement of bioprocess monitoring: development of novel concepts
Authors: Clementschitsch Franz , Bayer Karl
Published: May 2006

The advancement of bioprocess monitoring will play a crucial role to meet the future requirements of bioprocess technology. Major issues are the acceleration of process development to reduce the time to the market and to ensure optimal exploitation of the cell factory and further to cope with the requirements of the Process Analytical Technology initiative. Due to the enormous complexity of cellular systems and lack of appropriate sensor systems microbial production processes are still poorly understood. This holds generally true for the most microbial production processes, in particular for the recombinant protein production due to strong interaction between recombinant gene expression and host cell metabolism. Therefore, it is necessary to scrutinise the role of the different cellular compartments in the biosynthesis process in order to develop comprehensive process monitoring concepts by involving the most significant process variables and their interconnections. Although research for the development of novel sensor systems is progressing their applicability in bioprocessing is very limited with respect to on-line and in-situ measurement due to specific requirements of aseptic conditions, high number of analytes, drift, and often rather low physiological relevance. A comprehensive survey of the state of the art of bioprocess monitoring reveals that only a limited number of metabolic variables show a close correlation to the currently explored chemical/physical principles. In order to circumvent this unsatisfying situation mathematical methods are applied to uncover "hidden" information contained in the on-line data and thereby creating correlations to the multitude of highly specific biochemical off-line data. Modelling enables the continuous prediction of otherwise discrete off-line data whereby critical process states can be more easily detected. The challenging issue of this concept is to establish significant on-line and off-line data sets. In this context, online sensor systems are reviewed with respect to commercial availability in combination with the suitability of offline analytical measurement methods. In a case study, the aptitude of the concept to exploit easily available online data for prediction of complex process variables in a recombinant E. coli fed-batch cultivation aiming at the improvement of monitoring capabilities is demonstrated. In addition, the perspectives for model-based process supervision and process control are outlined.
Biosynthesis of isoprenoids, polyunsaturated fatty acids and flavonoids in Saccharomyces cerevisiae
Authors: Chemler Joseph A , Yan Yajun , Koffas Mattheos AG
Published: May 2006

Industrial biotechnology employs the controlled use of microorganisms for the production of synthetic chemicals or simple biomass that can further be used in a diverse array of applications that span the pharmaceutical, chemical and nutraceutical industries. Recent advances in metagenomics and in the incorporation of entire biosynthetic pathways into Saccharomyces cerevisiae have greatly expanded both the fitness and the repertoire of biochemicals that can be synthesized from this popular microorganism. Further, the availability of the S. cerevisiae entire genome sequence allows the application of systems biology approaches for improving its enormous biosynthetic potential. In this review, we will describe some of the efforts on using S. cerevisiae as a cell factory for the biosynthesis of high-value natural products that belong to the families of isoprenoids, flavonoids and long chain polyunsaturated fatty acids. As natural products are increasingly becoming the center of attention of the pharmaceutical and nutraceutical industries, the use of S. cerevisiae for their production is only expected to expand in the future, further allowing the biosynthesis of novel molecular structures with unique properties.
Comparison of coverage with insecticide-treated nets in a Tanzanian town and villages where nets and insecticide are either marketed or provided free of charge
Authors: Maxwell CA , Rwegoshora RT , Magesa SM , Curtis CF
Published: May 2006

Background

There is much emphasis on social marketing as a means of scaling up coverage with insecticide-treated nets and the question has arisen whether nets provided free-of-charge will be looked after by householders.

Methods

Over several years questionnaires and surveys of usage and condition of nets were carried out throughout a town and 15 villages in north-east Tanzania, where nets and insecticide have to be purchased and in 24 other villages where over 15000 nets had been donated and annual re-treatment is provided free-of-charge.

Results

There was very high population coverage in the town but, in the villages where nets have to be purchased, only 9.3% of people used nets which were intact and/or had been insecticide-treated and could, therefore, provide protection. However, where nets had been provided free, over 90% of the nets were still present and were brought for re-treatment several years later.

Conclusion

In this part of Tanzania, social marketing has performed well in a town but very poorly in villages. However, the study showed that people look after and bring for re-treatment nets which had been provided free-of-charge.
Measuring inequality: tools and an illustration
Authors: Williams Ruth FG , Doessel DP
Published: May 2006

Background

This paper examines an aspect of the problem of measuring inequality in health services. The measures that are commonly applied can be misleading because such measures obscure the difficulty in obtaining a complete ranking of distributions. The nature of the social welfare function underlying these measures is important. The overall object is to demonstrate that varying implications for the welfare of society result from inequality measures.

Method

Various tools for measuring a distribution are applied to some illustrative data on four distributions about mental health services. Although these data refer to this one aspect of health, the exercise is of broader relevance than mental health. The summary measures of dispersion conventionally used in empirical work are applied to the data here, such as the standard deviation, the coefficient of variation, the relative mean deviation and the Gini coefficient. Other, less commonly used measures also are applied, such as Theil's Index of Entropy, Atkinson's Measure (using two differing assumptions about the inequality aversion parameter). Lorenz curves are also drawn for these distributions.

Results

Distributions are shown to have differing rankings (in terms of which is more equal than another), depending on which measure is applied.

Conclusion

The scope and content of the literature from the past decade about health inequalities and inequities suggest that the economic literature from the past 100 years about inequality and inequity may have been overlooked, generally speaking, in the health inequalities and inequity literature. An understanding of economic theory and economic method, partly introduced in this article, is helpful in analysing health inequality and inequity.
Update: cohort mortality study of workers highly exposed to polychlorinated biphenyls (PCBs) during the manufacture of electrical capacitors, 1940-1998
Authors: Prince Mary M , Hein Misty J , Ruder Avima M , Waters Martha A , Laber Patricia A , Whelan Elizabeth A
Published: May 2006

Background

The National Institute for Occupational Safety and Health previously reported mortality for a cohort of workers considered highly exposed to polychlorinated biphenyls (PCBs) between 1939 and 1977 at two electrical capacitor manufacturing plants. The current study updated vital status, examined liver and rectal cancer mortality previously reported in excess in this cohort and evaluated mortality from non-Hodgkin's lymphoma (NHL) and cancers of the stomach, intestine, breast, prostate, skin (melanoma) and brain reported to be in excess in other cohort and case-control studies of PCB-exposed persons.

Methods

Mortality was updated through 1998 for 2572 workers. Age-, gender-, race- and calendar year-adjusted standardized mortality ratios (SMRs) and 95% confidence intervals (CI) were calculated using U.S., state and county referent rates. SMRs using U.S. referent rates are reported. Duration of employment was used as a surrogate for exposure.

Results

Consistent with the previous follow-up, mortality from biliary passage, liver and gall bladder cancer was significantly elevated (11 deaths, SMR 2.11, CI 1.05 – 3.77), but mortality from rectal cancer was not (6 deaths, SMR 1.47, CI 0.54 – 3.21). Among women, mortality from intestinal cancer (24 deaths, SMR 1.89, CI 1.21 – 2.82) and from "other diseases of the nervous system and sense organs", which include Parkinson's disease and amyotrophic lateral sclerosis, (15 deaths, SMR 2.07, CI 1.16 – 3.42) were elevated. There were four ALS deaths, all women (SMR 4.35, CI 1.19–11.14). Mortality was elevated for myeloma (7 deaths, SMR 2.11, CI 0.84 – 4.34), particularly among workers employed 10 years or more (5 deaths, SMR 2.80, CI 0.91 – 6.54). No linear associations between mortality and duration of employment were observed for the cancers of interest.

Conclusion

This update found that the earlier reported excess in this cohort for biliary, liver and gall bladder cancer persisted with longer follow-up. Excess mortality for intestinal cancer among women was elevated across categories of duration of employment; myeloma mortality was highest among those working 10 years or more. The small numbers of deaths from liver and intestinal cancers, myeloma and nervous system diseases coupled with the lack of an exposure-response relationship with duration of employment preclude drawing definitive conclusions regarding PCB exposure and these causes of death.
Negative impact of chronic obstructive pulmonary disease on the health-related quality of life of patients. Results of the EPIDEPOC study
Authors: Garrido Pilar Carrasco , Díez Javier de Miguel , Gutiérrez Javier Rejas , Centeno Antonio Martín , Vázquez Elena Gobartt , de Miguel Ángel Gil , Carballo Marta García , García Rodrigo Jiménez
Published: May 2006

Background

COPD is currently the fourth cause of morbidity and mortality in the developed world. Patients with COPD experience a progressive deterioration and disability, which lead to a worsening in their health-related quality of life (HRQoL). The aim of this work is to assess the Health-Related Quality of Life (HRQoL) of patients with stable COPD followed in primary care and to identify possible predictors of disease.

Methods

It is a multicenter, epidemiological, observational, descriptive study. Subjects of both sexes, older than 40 years and diagnosed of COPD at least 12 months before starting the study were included. Sociodemographic data, severity of disease, comorbidity, and use of health resources in the previous 12 months were collected. All patients were administered a generic quality-of-life questionnaire, the SF-12, that enables to calculate two scores, the physical (PCS-12) and the mental (MCS-12) component summary scores.

Results

10,711 patients were evaluated (75.6% men, 24.4% women), with a mean age of 67.1 years (SD 9.66). The mean value of FEV1was 35.9 ± 10.0%. Mean PCS-12 and MCS-12 scores were 36.0 ± 9.9 and 48.3 ± 10.9, respectively. Compared to the reference population, patients with COPD had a reduction of PCS-12, even in mild stages of the disease. The correlation with FEV1was higher for PCS-12 (r = 0.38) than for MCS-12 (r = 0.12). Predictors for both HRQoL components were sex, FEV1, use of oxygen therapy, and number of visits to emergency rooms and hospital admissions. Other independent predictors of PCS-12 were age, body mass index and educational level.

Conclusion

Patients with stable COPD show a reduction of their HRQoL, even in mild stages of the disease. The factors determining the HRQoL include sex, FEV1, use of oxygen therapy, and number of visits to emergency rooms and hospital admissions.
Biological efficacy of low versus medium dose aspirin after coronary surgery: results from a randomized trial [NCT00262275]
Authors: Lim Eric , Cornelissen Jacqueline , Routledge Tom , Ali Ayyaz , Kirtland Stephen , Sharples Linda , Sheridan Kate , Bellm Sarah , Munday Helen , Large Stephen
Published: May 2006

Background

The beneficial effect of aspirin after coronary surgery is established; however, a recent study reported the inability of low doses (100 mg) to inhibit postoperative platelet function. We conducted a double-blind randomised trial to establish the efficacy of low dose aspirin and to compare it against medium dose aspirin.

Methods

Patients undergoing coronary surgery were invited to participate and consenting patients were randomised to 100 mg or 325 mg of aspirin daily for 5 days. Our primary outcome was the difference in platelet aggregation (day 5 – baseline) using 1 μg/ml of collagen. Secondary outcomes were differences in EC50 of collagen, ADP and epinephrine (assessed using the technique of Born).

Results

From September 2002 to April 2004, 72 patients were randomised; 3 patients discontinued, leaving 35 and 34 in the low and medium dose aspirin arms respectively. The mean aggregation (using 1.1 μg/ml of collagen) was reduced in both the medium and low dose aspirin arms by 37% and 36% respectively. The baseline adjusted difference (low – medium) was 6% (95% CI -3 to 14; p = 0.19). The directions of the results for the differences in EC50 (low – medium) were consistent for collagen, ADP and epinephrine at -0.07 (-0.53 to 0.40), -0.08 (-0.28 to 0.11) and -4.41 (-10.56 to 1.72) respectively, but none were statistically significant.

Conclusion

Contrary to recent findings, low dose aspirin is effective and medium dose aspirin did not prove superior for inhibiting platelet aggregation after coronary surgery.
Combined fluticasone propionate and salmeterol reduces RSV infection more effectively than either of them alone in allergen-sensitized mice
Authors: Singam Rajeswari , Jena Prasanna K , Behera Sumita , Hellermann Gary R , Lockey Richard F , Ledford Dennis , Mohapatra Shyam S
Published: May 2006

Background

Respiratory syncytial virus (RSV) infection is the major cause of bronchiolitis in infants and is a risk factor for the development of asthma. Allergic asthmatics are more susceptible to RSV infection and viral exacerbation.

Methods

Since the effectiveness of corticosteroids in treating RSV infection has been controversial, we tested fluticasone propionate (FP) and salmeterol (Sal) alone versus FP plus Sal (FPS) on RSV-induced airway inflammation. Mice were sensitized and challenged with ovalbumin (OVA) and infected with RSV. Following infection they were treated with FP, Sal, or FPS intranasally and airway hyperreactivity (AHR), inflammation and RSV titers were examined.

Results

The group treated with FPS showed significantly lower AHR compared to the group treated with FP or Sal alone. The group treated with FP alone showed slightly decreased (non-significant) AHR compared to controls. Treatment with FPS resulted in significant decreases in the percentage of eosinophils and neutrophils in bronchoalveolar lavage fluid and in lung pathology compared to FP or Sal. FP alone decreased eosinophils but not neutrophils or lymphocytes, while Sal alone decreased eosinophils and neutrophils but not lymphocytes. FPS treatment of mice infected with RSV in the absence of allergen sensitization resulted in a 50% decrease of RSV titer in the lung and a reduction in neutrophils compared to FP or Sal.

Conclusion

Together, these results indicate that fluticasone in combination with salmeterol is a more effective treatment for decreasing airway hyperreactivity and inflammation than either of them alone in allergen-sensitized, RSV-infected mice.