http://www.herbalscienceresearch.com//aggregator/categories/1 Herbal Science Research - aggregated feeds in category BMC Journals en http://www.ijbnpa.org/content/5/1/42 Background: Lack of regular physical activity and consequent sub-optimal bone mass acquisition in youth has been implicated as a primary cause of adult-onset osteoporosis. IMPACT was a behavioral theory-based 1.5 years randomized controlled field study aimed at increasing bone accretion in middle school girls. The objective of this study was to determine the intervention effects of the IMPACT program upon key physical and sedentary activity endpoints among schools that participated in the IMPACT study. Endpoints examined included weight bearing physical activity (WBPA); moderate to vigorous physical activity (MVPA); vigorous physical activity (VPA); MET (metabolic equivalent) - weighted WBPA and MVPA; sedentary activity; before/after-school physical activity; and weekend physical activity. Methods: Primary data analysis using a pretest-posttest control group design was conducted utilizing mixed model analysis of covariance. Data gathered from the IMPACT cohort from 2000-2002 were analyzed to determine baseline versus follow-up differences in activity endpoints. Confounders investigated included ethnicity, body mass index, menarcheal status, participation in 7th grade PE/athletics, friend / familial support and neighborhood safety. Results: Follow-up means were higher for participating intervention schools relative to control schools for all physical activity variables but were statistically significant only for the following variables: daily minutes of vigorous physical activity (mean difference between Intervention (I) and Control (C) = 6.00[arrow up]minutes, 95% CI = 5.82-6.18, p = 0.05), daily after school activity minutes (mean difference between I and C = 8.95[arrow up] minutes, 95% CI = 8.69-9.21, p = 0.04), and daily weekend activity minutes (mean difference between I and C = 19.00[arrow up] minutes, 95% CI = 18.40-19.60, p = 0.05). The intervention significantly reduced duration of student daily TV/Video watching (mean difference between I and C = 12.11[arrow down] minutes, 95% CI = 11.74-12.48, p = 0.05) and total daily sedentary activity minutes (mean difference between I and C = 16.99[arrow down]minutes, 95% CI = 16.49-17.50, p = 0.04). Conclusion: A well designed and implemented school based health and physical activity intervention can result in a positive influence upon increasing physical activity levels and decreasing sedentary activity. Future interventions should consider a more structured intervention component to obtain significant changes in WBPA. Thu, 21 Aug 2008 00:00:00 -0700 http://breast-cancer-research.com/content/10/4/R71 IntroductionRelaxin is increased in human breast cancer and was shown to promote cancer cell migration in carcinoma cells of the breast, prostate and thyroid. In estrogen receptor alpha-negative MDA-MB-231 human breast cancer cells, relaxin was shown to down-regulate the metastasis-promoting protein S100A4 (metastasin), a highly significant prognostic factor for poor survival in breast cancer patients. The cellular mechanisms of relaxin exposure in breast cancer cells are not fully understood. The aim of this study was to investigate short-term and long-term effects of relaxin on cancer cell motility and S100A4 expression and to determine the long-term effects of relaxin on in vivo tumor growth in an estrogen-independent context. Methods: We have established stable transfectants of highly invasive estrogen receptor alpha-negative MDA-MB-231 human breast cancer cells with constitutive expression of bioactive H2-relaxin (MDA/RLN2). RLN2 secretion was determined by ELISA. Relaxin receptor RXFP1 (Relaxin-family-peptide) was detected by RT-PCR and its activation was assessed by induction of cyclic-AMP. Stable MDA/RLN2 clones and RLN2 treated MDA-MB-231 cells were subjected to motility and in vitro-invasion assays. Proliferation was assessed in bromodeoxyuridine (BrdU) and MTT assays. S100A4 expression was determined by RT-PCR and Western Blot. Specific small interfering RNA was employed to down-regulate relaxin receptor and S100A4. MDA/EGFP vector control and two MDA/RLN2 clones were injected subcutaneously in nude mice to determine tumor growth and cancer cell invasiveness in vivo. Xenograft tumor tissues were assessed by histology and immunohistochemistry and frozed tissues were used for the detection of S100A4 and RLN2. Results: Short-term exposure to relaxin for 24 hours increased cell motility in a relaxin receptor-dependent manner. This increase in cell motility was mediated by S100A4. Long-term exposure to relaxin secreted from stable transfectants reduced cell motility and in vitro invasiveness. Relaxin decreased cell proliferation and down-regulated cellular S100A4 levels in MDA-MB-231 and T47D breast cancer cells. Stable MDA/RLN2 transfectants produced smaller xenograft tumors containing reduced S100A4 protein levels in vivo. Conclusions: Our results indicate that long-term exposure to relaxin confers growth inhibitory and anti-invasive properties in estrogen-independent tumors in vivo which may in part be mediated through a down-regulation of S100A4. Thu, 21 Aug 2008 00:00:00 -0700 http://www.biomedcentral.com/1471-2393/8/40 Background: Postpartum hemorrhage (PPH) remains a major killer of women worldwide. Standard uterotonic treatments used to control postpartum bleeding do not always work and are not always available. Misoprostol's potential as a treatment option for PPH is increasingly known, but its use remains ad hoc and available evidence does not support the safety or efficacy of one particular regimen. This study aimed to determine the adjunct benefit of misoprostol when combined with standard oxytocics for PPH treatment. Methods: A randomized controlled trial was conducted in four Karachi hospitals from December 2005 - April 2007 to assess the benefit of a 600 mcg dose of misoprostol given sublingually in addition to standard oxytocics for postpartum hemorrhage treatment. Consenting women had their blood loss measured after normal vaginal delivery and were enrolled in the study after losing more than 500 ml of blood. Women were randomly assigned to receive either 600 mcg sublingual misoprostol or matching placebo in addition to standard PPH treatment with injectable oxytocics. Both women and providers were blinded to the treatment assignment. Blood loss was collected until active bleeding stopped and for a minimum of one hour after PPH diagnosis. Total blood loss, hemoglobin measures, and treatment outcomes were recorded for all participants. Results: Due to a much lower rate of PPH than expected (1.2%), only sixty-one patients were diagnosed and treated for their PPH in this study, and we were therefore unable to measure statistical significance in any of the primary endpoints. The addition of 600 mcg sublingual misoprostol to standard PPH treatments does, however, suggest a trend in reduced postpartum blood loss, a smaller drop in postpartum hemoglobin, and need for fewer additional interventions. Women who bled less overall had a significantly smaller drop in hemoglobin and received fewer additional interventions. There were no hysterectomies or maternal deaths among study participants. The rate of transient shivering and fever was significantly higher among women receiving misoprostol Conclusions: A 600 mcg dose of misoprostol given sublingually shows promise as an adjunct treatment for PPH and its use should continue to be explored for its life-saving potential in the care of women experiencing PPH. Trial Registration: Clinical trials.gov, Registry No. NCT00116480 Thu, 21 Aug 2008 00:00:00 -0700 http://www.biomedcentral.com/1741-7015/6/24 Malarial anaemia is an enormous public health problem in endemic areas and occurs predominantly in children in the first 3 years of life. Anaemia is due to both a great increase in clearance of uninfected cells and a failure of an adequate bone marrow response. Odhiambo, Stoute and colleagues show how the age distribution of malarial anaemia and the haemolysis of red blood cells may be linked by an age-dependent increase in the capacity of red blood cells to inactivate complement components absorbed or deposited directly on to the surface of the red blood cell. In this commentary, we discuss what has been established about the role of complement deposition on the surface of red blood cells in the pathology of malarial anaemia, how genetic polymorphisms of the complement control proteins influence the outcome of malaria infection and how the findings of Odhiambo, Stoute and colleagues and others shed light on the puzzling age distribution of different syndromes Thu, 21 Aug 2008 00:00:00 -0700 http://www.biomedcentral.com/1741-7015/6/23 Background: Severe anemia due to Plasmodium falciparum malaria is a major cause of mortality among young children in western Kenya. The factors that lead to the age-specific incidence of this anemia are unknown. Previous studies have shown an age-related expression of red cell complement regulatory proteins, which protect erythrocytes from autologous complement attack and destruction. Our primary objective was to determine whether in a malaria-endemic area red cells with low levels of complement regulatory proteins are at increased risk for complement (C3b) deposition in vivo. Secondarily, we studied the relationship between red cell complement regulatory protein levels and hemoglobin levels. Methods: Three hundred and forty-two life-long residents of a malaria-holoendemic region of western Kenya were enrolled in a cross-sectional study and stratified by age. We measured red cell C3b, CR1, CD55, and immune complex binding capacity by flow cytometry. Individuals who were positive for malaria were treated and blood was collected when they were free of parasitemia. Analysis of variance was used to identify independent variables associated with the %C3b-positive red cells and the hemoglobin level. Results: Individuals between the ages of 6 and 36 months had the lowest red cell CR1, highest %C3b-positive red cells, and highest parasite density. Malaria prevalence also reached its peak within this age group. Among children [less than or equal to]24 months of age the %C3b-positive red cells was usually higher in individuals who were treated for malaria than in uninfected individuals with similarly low red cell CR1 and CD55. The variables that most strongly influenced the %C3b-positive red cells were age, malaria status, and red cell CD55 level. Although it did not reach statistical significance, red cell CR1 was more important than red cell CD55 among individuals treated for malaria. The variables that most strongly influenced the hemoglobin level were age, the %C3b-positive red cells, red cell CR1, and red cell CD55. Conclusions: Increasing malaria prevalence among children >6 to [less than or equal to]36 months of age in western Kenya, together with low red cell CR1 and CD55 levels, results in increased C3b deposition on red cells and low hemoglobin. The strong contribution of age to C3b deposition suggests that there are still additional unidentified age-related factors that increase the susceptibility of red cells to C3b deposition and destruction. Thu, 21 Aug 2008 00:00:00 -0700 http://arthritis-research.com/content/10/4/R96 IntroductionThe biological basis for the avascular state of the intervertebral disc is not well understood. Previous work has suggested that the presence of thrombospondin-1 (TSP-1), a matricellular protein, in the outer annulus reflects a role for this protein in conferring an avascular status to the disc. In the present study we have examined TSP-2, a matricellular protein with recognized anti-angiogenic activity in vivo and in vitro. Methods: We examined both the location and expression of TSP-2 in the human disc, and its location in the disc and bordering soft tissues of five month-old normal wild type (WT) mice, and mice with a targeted disruption of the TSP-2 gene. Immunohistochemistry and quantitative histology were utilized in this study. Results: TSP-2 was found to be present in some, but not all, annulus cells of the human and mouse annulus. Although there was no difference in the number of disc cells in the annulus of TSP-2-null compared to that of WT animals, polarized light microscopy revealed a more irregular lamellar collagen structure in null compared to WT discs. Additionally, vascular beds at the margins of discs of TSP-2-null mice were substantially more irregular than those of WT animals. Counts of platelet endothelial cell adhesion molecule-1 (PECAM-1) -positive blood vessels in the tissue margin bordering the ventral annulus showed a significantly larger vascular bed in the tissue bordering the disc of TSP-2-null mice compared to that of WT mice (p = 0.0002). However, there was no vascular ingrowth into discs of the TSP-2-null mice. Conclusions: These data confirm a role for TSP-2 in the morphology of the disc and suggest the presence of other inhibitors of angiogenesis in the disc. We have shown that although an increase in vasculature was present in the TSP-2-null tissue in the margin of the disc, vascular ingrowth into the body of the disc did not occur. Our results point to the need for future research to understand the transition from the well-vascularized status of the fetal and young discs to the avascular state of the adult human or small mammalian disc. Thu, 21 Aug 2008 00:00:00 -0700 http://arthritis-research.com/content/10/4/R95 IntroductionHealth care utilization ("claims") databases contain information for millions of patients and provide important sources of information for a variety of study types. However, they typically do not contain information about disease severity. The goal of our study was to develop a health care claims index for rheumatoid arthritis (RA) severity using a previously developed medical records-based index for RA severity (RARBIS). Methods: The study population consisted of 120 patients from the Veteran's Administration (VA) Health System. We previously demonstrated the construct validity of the RARBIS and established its convergent validity with the Disease Activity Score (DAS-28). Potential claims-based indicators were entered into a linear regression model as independent variables and RARBIS as the dependent variable. The claims-based index for RA severity (CIRAS) was created using the coefficients from models with the highest R2 values selected by automated modeling procedures. To compare our claims-based index with our medical records-based index, we examined the correlation between the CIRAS and RARBIS using Spearman nonparametric tests. Results: The forward selection models yielded the highest model R2 for both the RARBIS with medications (R2=0.31) and the RARBIS without medications (R2=0.26). Components of the CIRAS included tests for inflammatory markers, number of chemistry panels and platelet counts ordered, rheumatoid factor, rehabilitation and rheumatology visits, and Felty's syndrome diagnosis. The CIRAS demonstrated moderate correlations with the RARBIS with medication and the RARBIS without medication subscales. Conclusions: We developed a health care claims-based index of RA severity (CIRAS) that showed moderate correlations with a previously validated records based index of severity. The CIRAS may serve as a potentially important tool in adjusting for RA severity in pharmacoepidemiology studies of RA treatment and complications using health care utilization data. Thu, 21 Aug 2008 00:00:00 -0700 http://arthritis-research.com/content/10/4/212 NF-kB is an inducible transcription factor controlled by two principal signaling cascades each activated by a set of signal ligands, the classical/canonical NF-kB activation pathway and the alternative/non-canonical pathway. The former pathway proceeds via phosphorylation and degradation of the IkB inhibitor protein and leads most commonly to activation of the heterodimer RelA/NF-kB1(p50) (Figs.1,2). The latter pathway proceeds via phosphorylation and proteolytic processing of NF-kB2(p100) and leads to activation, most commonly, of the heterodimer, RelB/NF-kB2(p52) (Figs. 1,3). Both pathways play critical roles at multiple levels of the immune system in health and in disease, including the autoimmune inflammatory response. These roles include cell-cycle progression, cell survival, adhesion and inhibition of apoptosis. NF-kB is constitutively activated in many autoimmune diseases including diabetes type 1, systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA). In this review we survey recent developments in the involvement of the classical and alternative pathways of NF-kB activation in autoimmunity, focusing particularly on RA. We discuss the involvement of NF-kB in self-reactive T and B lymphocyte development, survival and proliferation, also the maintenance of chronic inflammation due to cytokines such as TNF-alpha and IL-1. We emphasize the roles of IL-17 and Th17 cells in the inflammatory process and in the activation, maturation and proliferation of RA fibroblast-like synovial cells and differentiation and activation of bone resorbing activity of osteoclasts. The prospects of therapeutic intervention to block activation of the NF-kB signaling pathways in RA are also discussed. Thu, 21 Aug 2008 00:00:00 -0700 http://www.biomedcentral.com/1471-2334/8/113 Background: Rabies is a major public-health problem in developing countries such as China. Although the recent re-emergence of human rabies in China was noted in several epidemiological studies, little attention was paid to the reasons behind this phenomenon paralleling the findings of the previous reports. The purpose of this study is thus first to characterize the current trends of human rabies in China from 1990 to 2007, and then to define better recommendations for improving the post-exposure prophylaxis (PEP) schedules delivered to rabies patients. Methods: The most updated epidemiological data for 22527 human rabies cases from January 1990 to July 2007, retrieved from the surveillance database of reportable diseases managed by the Ministry of Health of China, were analysed. To investigate the efficiency for the post-exposure treatment of rabies, the details of 244 rabies patients, including their anti-rabies treatment of injuries or related incidents, were ascertained in Guangdong provincial jurisdiction. The risk factors to which the patients were predisposed or the regimens given to 80 patients who received any type of PEP were analysed to identify the reasons for the PEP failures. Results: The results from analysis of the large number of human rabies cases showed that rabies in China was largely under control during the period 1990-1996. However, there has been a large jump in the number of reported rabies cases since 2001 up to a new peak (with an incidence rate of 0.20 per 100000 people) that was reached in 2004, and where the level has remained until present. Then, we analysed the PEP in 244 rabies cases collected in the Guangdong province in 2003 and 2004, and found that 67.2% of the patients did not seek medical services or did not receive any PEP. Further analysis of PEP for the 80 rabies patients who received any type of PEP indicated that almost all of the patients did not receive proper or timely treatment on the wounds or post-exposure vaccination or rabies immunoglobulins. Thu, 21 Aug 2008 00:00:00 -0700 http://www.biomedcentral.com/1471-2407/8/244 Background: Part of the inherited risk to lung cancer is likely to include common, low risk alleles. The identification of this class of susceptibility is contingent on association-based analyses. We established GEnetic Lung CAncer Predisposition Study (GELCAPS) to collect DNA and clinico-pathological data from a large series of cases and a series of spouse/partner controls, thereby generating a key resource for the identification of low risk alleles. Methods: GELCAPS was one of the first genetic epidemiological trials in the UK to be adopted by the National Cancer Research Network (NCRN) onto its portfolio with the participation of over 100 oncology departments specialising in the management of lung cancer. Results: Samples from over 5,000 independent lung cancer cases and 2,000 controls have so far been assembled through GELCAPS. Conclusion: GELCAPS represents one of the largest datasets of its type in the world capable of informing on the contribution of low penetrance alleles to the development of lung cancer and the influence of genetic variation on outcome. In addition our experience in developing the GELCAPS serves to illustrate how large DNA biobanks for genetic analyses can be rapidly generated within the UK using the NCRN. Wed, 20 Aug 2008 00:00:00 -0700 http://www.biomedcentral.com/1471-2393/8/39 Background: The link between maternal factors and birth outcomes is well established. Substantial changes in society and medical care over time have influenced women's reproductive choices and health, subsequently affecting birth outcomes. The objective of this study was to describe temporal changes in key maternal and fetal factors affecting birth outcomes in Newcastle upon Tyne over three decades, 1961-1992. Methods: For these descriptive analyses we used data from a population-based birth record database constructed for the historical cohort Particulate Matter and Perinatal Events Research (PAMPER) study. The PAMPER database was created using details from paper-based hospital delivery and neonatal records for all births during 1961-1992 to mothers resident in Newcastle (out of a total of 109,086 singleton births, 97,809 hospital births with relevant information). In addition to hospital records, we used other sources for data collection on births not included in the delivery and neonatal records, for death and stillbirth registrations and for validation. Results: The average family size decreased mainly due to a decline in the proportion of families with 3 or more children. The distribution of mean maternal ages in all and in primiparous women was lowest in the mid 1970s, corresponding to a peak in the proportion of teenage mothers. The proportion of older mothers declined until the late 1970s (from 16.5% to 3.4%) followed by a steady increase. Mean birthweight in all and term babies gradually increased from the mid 1970s. The increase in the percentage of preterm birth paralleled a two-fold increase in the percentage of caesarean section among preterm births during the last two decades. The gap between the most affluent and the most deprived groups of the population widened over the three decades. Conclusions: Key maternal and fetal factors affecting birth outcomes, such as maternal age, parity, socioeconomic status, birthweight and gestational age, changed substantially during the 32-year period, from 1961 to 1992. The availability of accurate gestational age is extremely important for correct interpretation of trends in birthweight. Tue, 19 Aug 2008 00:00:00 -0700 http://www.biomedcentral.com/1471-2180/8/140 Background: Streptococcus agalactiae (Group B Streptococcus (GBS)) is an important human pathogen, particularly of new-borns. Emerging evidence for a relationship between genotype and virulence has accentuated the need for efficient and well-defined typing methods. The objective of this study was to develop a single nucleotide polymorphism (SNP) based method for assigning GBS isolates to multilocus sequence typing (MLST)-defined clonal complexes. Results: It was found that a SNP set derived from the MLST database on the basis of maximisation of Simpsons Index of Diversity provided poor resolution and did not define groups concordant with the population structure as defined by eBURST analysis of the MLST database. This was interpreted as being a consequence of low diversity and high frequency horizontal gene transfer. Accordingly, a different approach to SNP identification was developed. This entailed use of the "Not-N" bioinformatic algorithm that identifies SNPs diagnostic for groups of known sequence variants, together with an empirical process of SNP testing. This yielded a four member SNP set that divides GBS into 10 groups that are concordant with the population structure. A fifth SNP was identified that increased the sensitivity for the clinically significant clonal complex 17 clone to 100%. Kinetic PCR methods for the interrogation of these SNPs were developed, and used to genotype 116 well characterized isolates. Conclusions: A five SNP method for dividing GBS into biologically valid groups has been developed. These SNPs are ideal for high throughput surveillance activities, and combining with more rapidly evolving loci when additional resolution is required. Tue, 19 Aug 2008 00:00:00 -0700 http://www.biomedcentral.com/1471-2288/8/58 Background: The beta-binomial model is one of the methods that can be used to validly combine event rates from overdispersed binomial data. Our objective is to provide a full description of this method and to update and broaden its applications in clinical and public health research. Methods: We describe the statistical theories behind the beta-binomial model and the associated estimation methods. We supply information about statistical software that can provide beta-binomial estimations. Using a published example, we illustrate the application of the beta-binomial model when pooling overdispersed binomial data. Results: In an example regarding the safety of oral antifungal treatments, we had 41 treatment arms with event rates varying from 0% to 13.89%. Using the beta-binomial model, we obtained a summary event rate of 3.44% with a standard error of 0.59%. The parameters of the beta-binomial model took the values of 1.24 for alpha and 34.73 for beta. Conclusions: The beta-binomial model can provide a robust estimate for the summary event rate by pooling overdispersed binomial data from different studies. The explanation of the method and the demonstration of its applications should help researchers incorporate the beta-binomial method as they aggregate probabilities of events from heterogeneous studies. Tue, 19 Aug 2008 00:00:00 -0700 http://www.biomedcentral.com/1471-2172/9/49 Background: Interleukin 1 beta (IL-1beta) plays an important role in a number of chronic and acute inflammatory diseases. To understand the role of IL-1beta in disease processes and develop an in vivo screening system for anti-inflammatory drugs, a transgenic mouse line was generated which incorporated the transgene firefly luciferase gene driven by a 4.5-kb fragment of the human IL-1beta gene promoter. Luciferase gene expression was monitored in live mice under anesthesia using bioluminescence imaging in a number of inflammatory disease models. Results: In a LPS-induced sepsis model, dramatic increase in luciferase activity was observed in the mice. This transgene induction was time dependent and correlated with an increase of endogenous IL-1beta mRNA and pro-IL-1beta protein levels in the mice. In a zymosan-induced arthritis model and an oxazolone-induced skin hypersensitivity reaction model, luciferase expression was locally induced in the zymosan injected knee joint and in the ear with oxazolone application, respectively. Dexamethasone suppressed the expression of luciferase gene both in the acute sepsis model and in the acute arthritis model. Conclusions: Our data suggest that the transgenic mice model could be used to study transcriptional regulation of the IL-1beta gene expression in the inflammatory process and evaluation the effect of anti-inflammatory drug in vivo. Tue, 19 Aug 2008 00:00:00 -0700 http://www.biomedcentral.com/1471-2296/9/46 Background: The successful introduction of new methods for managing medically unexplained symptoms in primary care is dependent to a large degree on the attitudes, experiences and expectations of practitioners. As part of an exploratory randomised controlled trial of reattribution training, we sought the views of participating practitioners on patients with medically unexplained symptoms, and on the value of and barriers to the implementation of reattribution in practice. Methods: A nested attitudinal survey and qualitative study in sixteen primary care teams in north-west England. All practitioners participating in the trial (n=74) were invited to complete a structured survey. Semi-structured interviews were undertaken with a purposive sub-sample of survey respondents, using a structured topic guide. Interview transcripts were used to identify key issues, concepts and themes, which were grouped to construct a conceptual framework: this framework was applied systematically to the data. Results: Seventy (95%) of study participants responded to the survey. Survey respondents often found it stressful to work with patients with medically unexplained symptoms, though those who had received reattribution training were more optimistic about their ability to help them. Interview participants trained in reattribution (n=12) reported that reattribution increased their confidence to practice in a difficult area, with heightened awareness, altered perceptions of these patients, improved opportunities for team-building and transferable skills. However general practitioners also reported potential barriers to the implementation of reattribution in routine clinical practice, at the level of the patient, the doctor, the consultation, diagnosis and the healthcare context. Conclusions: Reattribution training increases practitioners' sense of competence in managing patients with medically unexplained symptoms. However, barriers to its implementation are considerable, and frequently lie outside the control of a group of practitioners generally sympathetic to patients with medically unexplained symptoms and the purpose of reattribution. These findings add further to the evidence of the difficulty of implementing reattribution in routine general practice. Tue, 19 Aug 2008 00:00:00 -0700 http://www.biomedcentral.com/1471-2105/9/347 Background: Rejection of false positive peptide matches in database searches of shotgun proteomic experimental data is highly desirable. Several methods have been developed to use the peptide retention time as to refine and improve peptide identifications from database search algorithms. This report describes the implementation of an automated approach to reduce false positives and validate peptide matches. Results: A robust linear regression based algorithm was developed to automate the evaluation of peptide identifications obtained from shotgun proteomic experiments. The algorithm scores peptides based on their predicted and observed reversed-phase liquid chromatography retention times. The robust algorithm does not require internal or external peptide standards to train or calibrate the linear regression model used for peptide retention time prediction. The algorithm is generic and can be incorporated into any database search program to perform automated evaluation of the candidate peptide matches based on their retention times. It provides a statistical score for each peptide match based on its retention time. Conclusions: Analysis of peptide matches where the retention time score was included resulted in a significant reduction of false positive matches with little effect on the number of true positives. Overall higher sensitivities and specificities were achieved for database searches carried out with MassMatrix, Mascot and X!Tandem after implementation of the retention time based score algorithm. Tue, 19 Aug 2008 00:00:00 -0700 http://www.biomedcentral.com/1471-2105/9/346 Background: The acceptor photobleaching fluorescence resonance energy transfer (FRET) method is widely used for monitoring molecular interactions in cells. This method of FRET, while among those with the simplest mathematics, is robust, self-controlled and independent of fluorophore amounts and ratios. Results: AccPbFRET is a user-friendly, efficient ImageJ plugin which allows fully corrected, pixel-wise calculation and detailed, ROI (region of interest)-based analysis of FRET efficiencies in microscopic images. Furthermore, automatic registration and semi-automatic analysis of large image sets is provided, which are not available in any existing FRET evaluation software. Conclusions: Despite of the widespread applicability of the acceptor photobleaching FRET technique, this is the first paper where all possible sources of major errors of the measurement and analysis are considered, and AccPbFRET is the only program which provides the complete suite of corrections - for registering image pairs, for unwanted photobleaching of the donor, for cross-talk of the acceptor and/or its photoproduct to the donor channel and for partial photobleaching of the acceptor. The program efficiently speeds up the analysis of large image sets even for novice users and is freely available. Tue, 19 Aug 2008 00:00:00 -0700 http://www.biomedcentral.com/1471-2334/8/112 Background: Neonatal tetanus (NT)is still considered as one of the major causes of neonatal death in many developing countries. The aim of the present study was to assess the characteristics of sixty-seven infants with the diagnosis of neonatal tetanus followed-up in the Pediatric Infectious Diseases Ward of Dicle University Hospital, Diyarbakir, between 1991 and 2006, and to draw to factors that may contribute (or may have contributed) to the elimination of the disease in Diyarbakir. Methods: The data of sixty-seven infants whose epidemiological and clinical findings were compatible with neonatal tetanus were reviewed. Patients were stratified into two groups according to whether they survived or not to assess the effect of certain factors in the prognosis. Factors having a contribution to the higher rate of tetanus among newborn infants were discussed. Results: A total of 55 cases of NT had been hospitalized between 1991 and 1996 whereas only 12 patients admitted in the last decade. All of the infants had been delivered at home by untrained traditional birth attendants (TBA), and none of the mothers had been immunized with tetanus toxoid during her pregnancy. Twenty-eight (41.8%) of the infants died during their follow-up. Lower birth weight, younger age at onset of symptoms and at the time admission, the presence of opisthotonus, risus sardonicus and were associated with a higher mortality rate. Conclusions: Although the number of neonatal tetanus cases admitted to our clinic in recent years is lower than in the last decade efforts including appropriate health education of the masses, ensurement of access to antenatal sevices and increasing the rate of tetanus immunization among mothers still should be made in our region to achieve the goal of neonatal tetanus elimination. Tue, 19 Aug 2008 00:00:00 -0700 http://www.biomedcentral.com/1472-6882/8/50 Background: Complementary and alternative medicine (CAM) use is prevalent among HIV-infected patients to reduce the toxicity of antiretroviral therapy. Ginseng has been used for treatment of hyperglycemia and insulin resistance, a common side effect of some HIV-1 protease inhibitors (PI). However, it is unknown whether American ginseng (AG) can reverse insulin resistance induced by the PI indinavir (IDV), and whether these two agents interact pharmacologically. We evaluated potential pharmacokinetic interactions between indinavir and AG, and assessed whether AG improves IDV-induced insulin resistance. Methods: After baseline assessment of insulin sensitivity using the insulin clamp technique, healthy volunteers received IDV 800 mg q8 h for 3 days and then IDV and AG 1g q8h for 14 days. IDV Pharmacokinetics and insulin sensitivity were assessed before and after AG co-administration. Results: There was no difference in the IDV area-under-the-curve after the co-administration of AG, compared to IDV alone (n=13). Although insulin-stimulated glucose disposal per unit of insulin (M/I) decreased by an average of 14.8 +/- 5.9% after 3 days of IDV (from 0.113 +/- 0.012 to 0.096 +/- 0.014 mg/kgFFM/min per muU/ml of insulin, p=0.03, n=11), M/I remained unchanged after co-administration of IDV and AG. Conclusions: IDV decreases insulin sensitivity, which is unaltered by AG co-administration. AG does not significantly affect IDV pharmacokinetics. Tue, 19 Aug 2008 00:00:00 -0700 http://www.biomedcentral.com/1471-2407/8/243 Background: Glioblastoma is the most lethal primary malignant brain tumor. Although considerable progress has been made in the treatment of this aggressive tumor, the clinical outcome for patients remains poor. Histone deacetylases (HDACs) are recognized as promising targets for cancer treatment. In the past several years, HDAC inhibitors (HDACis) have been used as radiosensitizers in glioblastoma treatment. However, no study has demonstrated the status of global HDAC expression in gliomas and its possible correlation to the use of HDACis. The purpose of this study was to evaluate and compare mRNA and protein levels of class I, II and IV of HDACs in low grade and high grade astrocytomas and normal brain tissue and to correlate the findings with the malignancy in astrocytomas. Methods: Forty-three microdissected patient tumor samples were evaluated. The histopathologic diagnoses were 20 low-grade gliomas (13 grade I and 7 grade II) and 23 high-grade gliomas (5 grade III and 18 glioblastomas). Eleven normal cerebral tissue samples were also analyzed (54 total samples analyzed). mRNA expression of class I, II, and IV HDACs was studied by quantitative real-time polymerase chain reaction and normalized to the housekeeping gene beta-glucuronidase. Protein levels were evaluated by western blotting. Results: We found that mRNA levels of class II and IV HDACs were downregulated in glioblastomas compared to low-grade astrocytomas and normal brain tissue (7 in 8 genes, p<0.05). The protein levels of class II HDAC9 were also lower in high-grade astrocytomas than in low-grade astrocytomas and normal brain tissue. Additionally, we found that histone H3 (but not histone H4) was more acetylated in glioblastomas than normal brain tissue. Conclusions: Our study establishes a negative correlation between HDAC gene expression and the glioma grade suggesting that class II and IV HDACs might play an important role in glioma malignancy. Evaluation of histone acetylation levels showed that histone H3 is more acetylated in glioblastomas than normal brain tissue confirming the downregulation of HDAC mRNA in glioblastomas. Tue, 19 Aug 2008 00:00:00 -0700 http://www.biomedcentral.com/1471-2288/8/57 Background: Some populations targeted in survey research can be hard to reach, either because of lack of contact information, or non-existent databases to inform sampling. Here, we present a methodological "case-report" of the yield of a multi-step survey study assessing views on health care among American emigres to Canada, a hard-to-reach population. Methods: To sample this hard-to-reach population, we held a live media conference, supplemented by a nation-wide media release announcing the study. We prepared an 'op-ed' piece describing the study and how to participate. We paid for advertisements in 6 newspapers. We sent the survey information to targeted organizations. And lastly, we asked those who completed the web survey to send the information to others. We use descriptive statistics to document the method's yield. Results: The combined media strategies led to 4 television news interviews, 10 newspaper stories, 1 editorial and 2 radio interviews. 458 unique individuals accessed the on-line survey, among whom 310 eligible subjects provided responses to the key study questions. Fifty-six percent reported that they became aware of the survey via media outlets, 26 percent by word of mouth, and 9 percent through both the media and word of mouth. Conclusions: Our multi-step communication method yielded a sufficient sample of Americans living in Canada. This combination of paid and unpaid media exposure can be considered by others as a unique methodological approach to identifying and sampling hard-to-reach populations. Mon, 18 Aug 2008 00:00:00 -0700 http://www.biomedcentral.com/1471-2288/8/56 Background: Results from clinical trials are usually summarized in the form of sampling distributions. When full information (mean, SEM) about these distributions is given, performing meta-analysis is straightforward. However, when some of the sampling distributions only have mean values, a challenging issue is to decide how to use such distributions in meta-analysis. Currently, the most common approaches are either ignoring such trials or for each trial with a missing SEM, finding a similar trial and taking its SEM value as the missing SEM. Both approaches have drawbacks. As an alternative, this paper develops and tests two new methods, the first being the prognostic method and the second being the interval method, to estimate any missing SEMs from a set of sampling distributions with full information. A merging method is also proposed to handle clinical trials with partial information to simulate meta-analysis. Methods: Both of our methods use the assumption that the samples for which the sampling distributions will be merged are randomly selected from the same population. In the prognostic method, we predict the missing SEMs from the given SEMs. In the interval method, we define intervals that we believe will contain the missing SEMs and then we use these intervals in the merging process. Results: Two sets of clinical trials are used to verify our methods. One family of trials is on comparing different drugs for reduction of low density lipprotein cholesterol (LDL) for Type-2 diabetes, and the other is about the effectiveness of drugs for lowering intraocular pressure (IOP). Both methods are shown to be useful for approximating the conventional meta-analysis including trials with incomplete information. For example, the meta-analysis result of Latanoprost versus Timolol on IOP reduction for six months provided in [1] was 5:05+/-1.15 (Mean+/-SEM) with full information. If the last trial in this study is assumed to be with partial information, the traditional analysis method for dealing with incomplete information that ignores this trial would give 6:49 +/- 1:36 while our prognostic method gives 5:02+/-1.15, and our interval method provides two intervals as Mean [4:25; 5:63] and SEM [1:01; 1:24]. Conclusions: Both the prognostic and the interval methods are useful alternatives for dealing with missing data in meta-analysis. We recommend clinicians to use the prognostic method to predict the missing SEMs in order to perform meta-analysis and the interval method for obtaining a more cautious result. Mon, 18 Aug 2008 00:00:00 -0700 http://www.biomedcentral.com/1471-2121/9/46 Background: The normal growth and function of mammary epithelial cells depend on interactions with the supportive stroma. Alterations in this communication can lead to the progression or expansion of malignant growth. The human mammary gland contains two distinctive types of fibroblasts within the stroma. The epithelial cells are surrounded by loosely connected intralobular fibroblasts, which are subsequently surrounded by the more compacted interlobular fibroblasts. The different proximity of these fibroblasts to the epithelial cells suggests distinctive functions for these two subtypes. In this report, we compared the gene expression profiles between the two stromal subtypes. Methods: Fresh normal breast tissue was collected from reduction mammoplasty patients and immediately placed into embedding medium and frozen on dry ice. Tissue sections were subjected to laser capture microscopy to isolate the interlobular from the intralobular fibroblasts. RNA was prepared and subjected to microarray analysis using the Affymetrix Human Genome U133 GeneChip. Data was analyzed using the Affy and Limma packages available from Bioconductor. Findings from the microarray analysis were validated by RT-PCR and immunohistochemistry. Results: No statistically significant difference was detected between the gene expression profiles of the interlobular and intralobular fibroblasts by microarray analysis and RT-PCR. However, for some of the genes tested, the protein expression patterns between the two subtypes of fibroblasts were significantly different. Conclusions: This study is the first to report the gene expression profiles of the two distinct fibroblast populations within the human mammary gland. While there was no significant difference in the gene expression profiles between the groups, there was an obvious difference in the expression pattern of several proteins tested. This report also highlights the importance of studying gene regulation at both the transcriptional and post-translational level. Mon, 18 Aug 2008 00:00:00 -0700 http://www.biomedcentral.com/1471-2105/9/345 Background: Repbase is a reference database of eukaryotic repetitive DNA, which includes prototypic sequences of repeats and basic information described in annotations. Repbase already has software for entering new sequence families and for comparing the user's sequence with the database of consensus sequences. Results: We describe the software named VisualRepbase and the associated database, which allow for displaying and analyzing all occurrences of transposable element families present in an annotated genome. VisualRepbase is a Java-based interface which can download selected occurrences of transposable elements, show the distribution of given families on the chromosome, and present the localization of these occurrences with regard to gene annotations and other families of transposable elements in Repbase. In addition, it has several features for saving the graphical representation of occurrences, saving all sequences in FASTA format, and searching and saving all annotated genes that are surrounded by these occurrences. Conclusions: VisualRepbase is available as a downloadable version. It can be found at http://girinst.org/repbase/update/visual repbase.html. Mon, 18 Aug 2008 00:00:00 -0700 http://www.biomedcentral.com/1471-2105/9/344 Background: Understanding how proteins fold is essential to our quest in discovering how life works at the molecular level. Current computation power enables researchers to produce a huge amount of folding simulation data. Hence there is a pressing need to be able to interpret and identify novel folding features from them. Results: In this paper, we model each folding trajectory as a multi-dimensional curve. We then develop an effective multiple curve comparison (MCC) algorithm, called the enhanced partial order (EPO) algorithm, to extract features from a set of diverse folding trajectories, including both successful and unsuccessful simulation runs. The EPO algorithm addresses several new challenges presented by comparing high dimensional curves coming from folding trajectories. A detailed case study on miniprotein Trp-cage demonstrates that our algorithm can detect similarities at rather low level, and extract biologically meaningful folding events. Conclusions: The EPO algorithm is general and applicable to a wide range of applications. We demonstrate its generality and effectiveness by applying it to aligning multiple protein structures with low similarities. For user's convenience, we provide a web server for the algorithm at http://db.cse.ohio-state.edu/EPO. Mon, 18 Aug 2008 00:00:00 -0700 http://www.biomedcentral.com/1471-2105/9/343 Background: Tiling arrays are an important tool for the study of transcriptional activity, protein-DNA interactions and chromatin structure on a genome-wide scale at high resolution. Although hidden Markov models have been used successfully to analyse tiling array data, parameter estimation for these models is typically ad hoc. Especially in the context of ChIP-chip experiments, no standard procedures exist to obtain parameter estimates from the data. Common methods for the calculation of maximum likelihood estimates such as the Baum-Welch algorithm or Viterbi training are rarely applied in the context of tiling array analysis. Results: Here we develop a hidden Markov model for the analysis of chromatin structure ChIP-chip tiling array data, using t emission distributions to increase robustness towards outliers. Maximum likelihood estimates are used for all model parameters. Two different approaches to parameter estimation are investigated and combined into an efficient procedure. Conclusion: We illustrate an efficient parameter estimation procedure that can be used for HMM based methods in general and leads to a clear increase in performance when compared to the use of ad hoc estimates. The resulting hidden Markov model outperforms established methods like TileMap in the context of histone modification studies. Mon, 18 Aug 2008 00:00:00 -0700 http://arthritis-research.com/content/10/4/R94 IntroductionThere is increasing evidence that autoantibodies and immune complexes (ICs) contribute to synovitis in rheumatoid arthritis (RA), yet the autoantigens incorporated in ICs in RA remain incompletely characterized. Methods: We utilized C1q to capture ICs from plasma derived from human RA and control patients, followed by detection with antibodies specific for: (i) immunoglobulin to detect ICs, and (ii) fibrinogen to detect fibrinogen-containing ICs. RA and control plasma were separated by liquid chromatography, and fractions characterized by ELISA, immunoblotting and mass spectrometry. Immunohistochemical staining was performed on rheumatoid synovial tissue. Results: C1q-immunoassays demonstrated increased levels of IgG (P = 0.01) and IgM (P = 0.0002) ICs in plasma derived from RA patients possessing anti-cyclic citrullinated peptide autoantibodies (CCP+) as compared to healthy controls. About one-half of the CCP+ RA possessed circulating ICs containing fibrinogen (P = 0.0004). Fractionation of whole RA plasma revealed citrullinated fibrinogen in the high molecular weight fractions that contained immune complexes. Positive correlations were observed between fibrinogen containing immune complex and anti-citrullinated fibrinogen autoantibodies, anti-CCP antibody, rheumatoid factor and certain clinical characteristics. Immunohistochemical staining demonstrated co-localization of fibrinogen, immunoglobulin and complement component C3 in RA pannus tissue. Mass spectrometry analysis of immune complexes immunoprecipitated from RA pannus tissue lysates demonstrated the presence of citrullinated fibrinogen. Conclusions: Circulating ICs containing citrullinated fibrinogen are present in one-half of CCP+ RA patients, and these immune complexes co-localize with C3 in the rheumatoid synovium suggesting that they contribute to synovitis in a subset of RA patients. Mon, 18 Aug 2008 00:00:00 -0700 http://arthritis-research.com/content/10/4/R93 IntroductionThis study was conducted to quantify the number of TH-17 cells present in rheumatoid arthritis (RA) synovial fluid (SF) and the to determine the level of IL-17 cytokine in RA, osteoarthritis (OA) and normal synovial tissue, as well as to examine SF macrophages for the presence of IL-23, IL-27 and interferon (IFN)-g. Methods: Peripheral blood (PB) mononuclear cells from normal and RA donors and mononuclear cells from RA SF were examined either without stimulation, or after pretreatment with IL-23 followed by stimulation with PMA plus ionomycin (P/I). The abundance of TH-17 cells in RA SF was determined by flow cytometry. IL-17 levels were quantified in synovial tissue from RA, OA and normal individuals by ELISA. IL-23 was identified in SFs by ELISA. RA SF and control in vitro differentiated macrophages were either untreated or treated with the Toll like receptor (TLR)2 ligand peptidoglycan, and then IL-23, IL-27 and IFN-g mRNA levels were quantified by real-time RT-PCR. Results: Treatment with P/I alone or combined with IL-23 significantly increased the number of TH-17 cells in normal and RA PB and in RA SF. With or without P/I plus IL-23, the percentage of TH-17 cells was higher in RA SF compared to normal and RA PB. IL-17 levels were comparable in OA and normal synovial tissues, and these values were significantly increased in RA synovial tissue. Although IL-17 was readily detected in RA SFs, IL-23 was rarely identified in RA SF. However, IL-23 mRNA was significantly increased in RA SF macrophages compared to control macrophages, with or without TLR2 ligation. IL-27 mRNA was also significantly higher in RA SF compared to control macrophages, but there was no difference in IL-27 levels between RA and control macrophages following TLR2 ligation. IFN-g mRNA was also detectable in RA SF macrophages but not control macrophages and the increase of IFN-g mRNA following TLR2 ligation was greater in RA SF macrophages compared to control macrophages. Conclusions: These observations support a role for TH-17 cells in RA. Our observations do not strongly support a role or IL-23 in the generation to TH-17 cells in the RA joint, however, they suggest that strategies which enhance IL-27 or IFN-g might modulate the presence of TH-17 cells in RA. Mon, 18 Aug 2008 00:00:00 -0700 http://www.biomedcentral.com/1471-2334/8/111 Background: Human herpesvirus 8 (HHV-8), cytomegalovirus (CMV) and Epstein-Barr virus (EBV) are prevalent in Africa, but less common elsewhere and the modes of transmission are still subject to debate. Generally, they rarely cause disease in the immunocompetent host but are highly oncogenic when associated with immunosuppression. Although the high prevalence of HHV-8, CMV and EBV has been well documented in Africa, such data are sparse from Ghana. Methods: Serum samples from 3275 HIV-seronegative healthy blood donors and 250 HIV-AIDS patients were tested for antibodies specific for HHV-8, CMV and EBV by IgG ELISA assays. Differences in seropositivity rates by gender and age were evaluated using the Chi-square test with Yates correction. Results: Of the 3275 HIV-seronegative healthy blood donors tested, 2573 (78.6%) were males and 702 (21.4%) were females, with ages ranging from 18 to 65 years (median 32.6; mean 31.2; mode 30). Of the 250 HIV-AIDS patients tested, 140 (56%) were males and 110 (44%) were females, with ages ranging from 17 to 64 years (median 30.8; mean 30.3; mode 28). Among the HIV-seronegative healthy blood donors, overall seroprevalence of HHV-8, CMV and EBV was 23.7%, 77.6% and 20.0%, respectively. Among the HIV-AIDS patients, overall seroprevalence of HHV-8, CMV and EBV was 65.6%, 59.2% and 87.2%, respectively. The seroprevalence of HHV-8 (p < 0.005) and EBV (p < 0.001) was statistically significantly higher in HIV-AIDS patients compared to HIV-seronegative healthy blood donors. There was no statistically significant difference (p = 0.24) between CMV seroprevalence in HIV-AIDS patients and HIV-seronegative healthy blood donors. Age and gender were not independent determinants (p > 0.05) for all three infections among HIV-seronegative healthy blood donors and HIV-AIDS patients in Ghana. Conclusions: The results presented herein indicate that HHV-8, CMV and EBV infections are hyperendemic in both HIV-seronegative and HIV-seropositive Ghanaians, and suggest primarily a horizontal route of transmission of these three viral infections in Ghana. Mon, 18 Aug 2008 00:00:00 -0700 http://www.biomedcentral.com/1472-6882/8/49 Background: We previously hypothesized that achievement of recovery of brain function after the injury requires the reconstruction of neuronal networks, including neurite regeneration and synapse reformation. Kihi-to is composed of twelve crude drugs, some of which have already been shown to possess neurite extension properties in our previous studies. The effect of Kihi-to on memory deficit has not been examined. Thus, the goal of the present study is to determine the in vivo and in vitro effects of Kihi-to on memory, neurite growth and synapse reconstruction. Methods: Effects of Kihi-to, a traditional Japanese-Chinese traditional medicine, on memory deficits and losses of neurites and synapses were examined using Alzheimer's disease model mice. Improvements of Abeta(25-35)-induced neuritic atrophy by Kihi-to and the mechanism were investigated in cultured cortical neurons. Results: Administration of Kihi-to for consecutive 3 days resulted in marked improvements of Abeta(25-35)-induced impairments in memory acquisition, memory retention, and object recognition memory in mice. Immunohistochemical comparisons suggested that Kihi-to attenuated neuritic, synaptic and myelin losses in the cerebral cortex, hippocampus and striatum. Kihi-to also attenuated the calpain increase in the cerebral cortex and hippocampus. When Kihi-to was added to cells 4 days after Abeta(25-35) treatment, axonal and dendritic outgrowths in cultured cortical neurons were restored as demonstrated by extended lengths of phosphorylated neurofilament-H (P-NF-H) and microtubule-associated protein (MAP)2-positive neurites. Abeta(25-35)-induced cell death in cortical culture was also markedly inhibited by Kihi-to. Since NF-H, MAP2 and myelin basic protein (MBP) are substrates of calpain, and calpain is known to be involved in Abeta-induced axonal atrophy, expression levels of calpain and calpastatin were measured. Treatment with Kihi-to inhibited the Abeta(25-35)-evoked increase in the calpain level and decrease in the calpastatin level. In addition, Kihi-to inhibited Abeta(25-35)-induced calcium entry. Conclusion: In conclusion Kihi-to clearly improved the memory impairment and losses of neurites and synapses. Sat, 16 Aug 2008 00:00:00 -0700