Harnessing naturally randomized transcription to infer regulatory relationships among genes

We develop an approach utilizing randomized genotypes to rigorously infer causal regulatory relationships among genes at the transcriptional level, based on experiments in which genotyping and expression profiling are performed. This approach can be used to build transcriptional regulatory networks and to identify putative regulators of genes. We apply the method to an experiment in yeast, in which genes known to be in the same processes and functions are recovered in the resulting transcriptional regulatory network.

Systematic review of the effect of diet and exercise lifestyle interventions in the secondary prevention of coronary heart disease.

The effectiveness of lifestyle interventions within secondary prevention of coronary heart disease(CHD)remains unclear.This systematic review aimed to determine their effectiveness and included randomized controlled trials of lifestyle interventions, in primary care or community settings, with a minimum follow-up of three months, published since 1990. 21 trials with 10,799 patients were included; the interventions were multifactorial (10), educational (4), psychological (3), dietary (1), organisational (2), and exercise(1). The overall results for modifiable risk factors suggested improvements in dietary and exercise outcomes but no overall effect on smoking outcomes. In trials that examined mortality and morbidity,significant benefits were reported for total mortality (in 4 of 6 trials;overall risk ratio(RR) 0.75 (95%confidence intervals (CI) 0.65, 0.87)), cardiovascular mortality (3 of 8 trials; overall RR 0.63(95%CI 0.47, 0.84)), and nonfatal cardiac events(5 of 9 trials; overall RR 0.68(95%CI 0.55, 0.84)). The heterogeneity between trials and generally poor quality of trials make any concrete conclusions difficult. However, the beneficial effects observed in this review are encouraging and should stimulate further research.

Treatment Foster Care for Improving Outcomes in Children and Young People: A Systematic Review

Objective: To assess the impact of treatment foster care (TFC) on psychosocial and behavioral outcomes, delinquency, placement stability, and discharge status for children and adolescents who, for reasons of severe medical, social, psychological and behavioural problems, were placed in out-of-home care in restrictive settings or at risk of placement in such settings. Method: Electronic bibliographic databases, web searches, and article reference lists were used to identify randomized controlled trials (RCTs) investigating the effectiveness of TFC with children and young people. The Cochrane Collaboration’s criteria were used to assess the methodological quality of studies that met the inclusion criteria. Wherever possible, extracted outcome data from similar studies were synthesized with random effects meta-analyses. Results: A total of 5 studies including 390 participants were included in this review. Data suggest that TFC may be a useful intervention for children and young people with complex emotional, psychological, and behavioural need, who are at risk of placements in nonfamily settings that restrict their liberty and opportunities for social inclusion. Conclusion: Although the inclusion criteria for this systematic review set a study design threshold higher than that of previous reviews, the findings mirror those of earlier reviews. While the results of individual studies generally indicate that TFC is a promising intervention for children and youth experiencing mental health problems, behavioral problems, or problems of delinquency, the evidence base is not robust and more research is needed due to the limited number of studies in this area.

Healthcare professional experiences and attitudes on unlicensed/off-label paediatric prescribing and paediatric clinical trials.

Objectives: To investigate the knowledge and views of a range of healthcare professionals (consultant paediatricians, general practitioners (GPs), community pharmacists and paediatric nurses) regarding the use of unlicensed/off-label medicines in children and the participation of children in clinical trials.

Methods: A regional study in which a survey instrument with 39 items was issued to 500 randomly selected GPs, all community pharmacists (n?=?512), 50 hospital consultants and 150 paediatric nurses in Northern Ireland.

Results: Approximately half (46.5%) of the 1,212 healthcare professionals approached responded to the questionnaire. The majority of respondents indicated their familiarity with the term unlicensed (82.9%) or off-label (58.6%) prescribing with the most frequently quoted reason for such prescribing being younger age (33.6%). Apart from community pharmacists, most respondents reported having gained their knowledge through personal experience. Even though a large percentage of respondents expressed concerns about the safety (77.8%) or efficacy (87.9%) of unlicensed/off-label prescribing in children, only 30.7% reported informing parents/guardians of these concerns on the use of such medicines in children. In addition, only 56% of respondents believed that unlicensed/off-label medicines should undergo clinical trials in children. Overall, 28.4% of respondents (20.1% of GPs, 41.4% of community pharmacists, 27.7% of paediatric nurses and 94% of consultant paediatricians) indicated their willingness to be actively involved in, and recruit their patients for paediatric clinical research.

Conclusion: The use of unlicensed and off-label medicines remains a major issue in paediatric medicine. Until such times as more licensed medicines are available for children, clear guidance should be developed to allow consistency in practice across the spectrum of healthcare professionals who are involved with such medicines in their routine practice.

The Paediatric Rheumatology International Trials Organisation provisional criteria for the evaluation of response to therapy in juvenile dermatomyositis.

Objective To develop a provisional definition for the evaluation of response to therapy in juvenile dermatomyositis (DM) based on the Paediatric Rheumatology International Trials Organisation juvenile DM core set of variables. Methods Thirty-seven experienced pediatric rheumatologists from 27 countries achieved consensus on 128 difficult patient profiles as clinically improved or not improved using a stepwise approach (patient's rating, statistical analysis, definition selection). Using the physicians' consensus ratings as the “gold standard measure,” chi-square, sensitivity, specificity, false-positive and-negative rates, area under the receiver operating characteristic curve, and kappa agreement for candidate definitions of improvement were calculated. Definitions with kappa values >0.8 were multiplied by the face validity score to select the top definitions. Results The top definition of improvement was at least 20% improvement from baseline in 3 of 6 core set variables with no more than 1 of the remaining worsening by more than 30%, which cannot be muscle strength. The second-highest scoring definition was at least 20% improvement from baseline in 3 of 6 core set variables with no more than 2 of the remaining worsening by more than 25%, which cannot be muscle strength (definition P1 selected by the International Myositis Assessment and Clinical Studies group). The third is similar to the second with the maximum amount of worsening set to 30%. This indicates convergent validity of the process. Conclusion We propose a provisional data-driven definition of improvement that reflects well the consensus rating of experienced clinicians, which incorporates clinically meaningful change in core set variables in a composite end point for the evaluation of global response to therapy in juvenile DM.

Blood pressure lowering in patients without prior cerebrovascular disease for prevention of cognitive impairment and dementia

Background: This is an update of a previous review (McGuinness 2006). Hypertension and cognitive impairment are prevalent in older people. Hypertension is a direct risk factor for vascular dementia (VaD) and recent studies have suggested hypertension impacts upon prevalence of Alzheimer's disease (AD). Therefore does treatment of hypertension prevent cognitive decline?
Objectives: To assess the effects of blood pressure lowering treatments for the prevention of dementia and cognitive decline in patients with hypertension but no history of cerebrovascular disease.
Search strategy: The Specialized Register of the Cochrane Dementia and Cognitive Improvement Group, The Cochrane Library, MEDLINE, EMBASE, PsycINFO, CINAHL, LILACS as well as many trials databases and grey literature sources were searched on 13 February 2008 using the terms: hypertens$ OR anti-hypertens$. Selection criteria: Randomized, double-blind, placebo controlled trials in which pharmacological or non-pharmacological interventions to lower blood pressure were given for at least six months.
Data collection and analysis: Two independent reviewers assessed trial quality and extracted data. The following outcomes were assessed: incidence of dementia, cognitive change from baseline, blood pressure level, incidence and severity of side effects and quality of life.
Main results: Four trials including 15,936 hypertensive subjects were identified. Average age was 75.4 years. Mean blood pressure at entry across the studies was 171/86 mmHg. The combined result of the four trials reporting incidence of dementia indicated no significant difference between treatment and placebo (236/7767 versus 259/7660, Odds Ratio (OR) = 0.89, 95% CI 0.74, 1.07) and there was considerable heterogeneity between the trials. The combined results from the three trials reporting change in Mini Mental State Examination (MMSE) did not indicate a benefit from treatment (Weighted Mean Difference (WMD) = 0.42, 95%CI 0.30, 0.53). Both systolic and diastolic blood pressure levels were reduced significantly in the three trials assessing this outcome (WMD = -10.22, 95% CI -10.78, -9.66 for systolic blood pressure, WMD = -4.28, 95% CI -4.58, -3.98 for diastolic blood pressure). Three trials reported adverse effects requiring discontinuation of treatment and the combined results indicated no significant difference (OR = 1.01, 95% CI 0.92, 1.11). When analysed separately, however, more patients on placebo in Syst Eur 1997 were likely to discontinue treatment due to side effects; the converse was true in SHEP 1991. Quality of life data could not be analysed in the four studies. Analysis of the included studies in this review was problematic as many of the control subjects received antihypertensive treatment because their blood pressures exceeded pre-set values. In most cases the study became a comparison between the study drug against a usual antihypertensive regimen.
Authors' conclusions: There is no convincing evidence fromthe trials identified that blood pressure lowering in late-life prevents the development of dementia or cognitive impairment in hypertensive patients with no apparent prior cerebrovascular disease. There were significant problems identified with analysing the data, however, due to the number of patients lost to follow-up and the number of placebo patients who received active treatment. This introduced bias. More robust results may be obtained by conducting a meta-analysis using individual patient data.

Statins for the prevention of dementia

Background: This is an update of a Cochrane review first published in 2001. At that stage there was insufficient evidence to recommend statins for the prevention of Alzheimer's disease (AD). The scope of this review has been expanded to include all forms of dementia.
Objectives: To assess the effects of statins in the prevention of dementia.
Search strategy: The Specialized Register of the Cochrane Dementia and Cognitive Improvement Group, The Cochrane Library, MEDLINE, EMBASE, PsycINFO, CINAHL and LILACS were searched on 10 October 2007 using the terms statin*, lovastatin*, pravastatin*, simvastatin*, fluvastatin*, atorvastatin* and rosuvastatin*. The CDCIG Register contains records from many healthcare databases, SIGLE, LILACS as well as many trials databases and is updated regularly.
Selection criteria: Double-blind randomized placebo-controlled trials of statins in people at risk of AD and dementia.
Data collection and analysis: Two independent reviewers extracted and assessed data independently and agreement was reached after discussion. Adverse effects were noted.
Main results: Two trials were identified with 26,340 participants; HPS 2002 and PROSPER 2002. Age range was 40-82 years across the two studies, PROSPER 2002 included 5804 patients aged 70-82 years and HPS included 20,536 patients with 5806 at least 70 years old at study entry. Mean total cholesterol 5.9 mmol/l, LDL cholesterol 3.4 mmol/l at study entry with mean reduction in LDL cholesterol of 1.0mmol/l in simvastatin treated patients compared to placebo in HPS 2002. Mean total cholesterol 5.7 mmol/l, LDL cholesterol 3.8 mmol/l at study entry with mean reduction in LDL cholesterol of 1.02 mmol/l in pravastatin treated patients compared to placebo in PROSPER 2002. Mean follow-up 3.2 years in PROSPER, 5 years in HPS 2002. Cognition was measured at different times and with different scales so could not be combined in a meta-analysis. There was no difference in incidence of dementia in HPS 2002 (31 cases in simvastatin group, 31 cases in placebo group) nor in performance on the modified Telephone Interview for Cognitive Status at final follow-up (23.7% simvastatin group cognitively impaired vs 24.2% in placebo group). There was no difference in cognition between groups either in relation to age at study entry or previous history of cerebrovascular disease. Cognitive function declined at the same rate in both treatment groups in PROSPER 2002, there was no significant difference between pravastatin treated and placebo groups in performance on letter digit codes, picture word learning test, Stroop and Mini Mental State Examination. There was no evidence that statins were detrimental to cognition.
Authors' conclusions : There is good evidence from RCTs that statins given in late life to individuals at risk of vascular disease have no effect in preventing AD or dementia. Biologically it seems feasible that statins could prevent dementia due to their role in cholesterol reduction and initial evidence from observational studies was very promising. Indication bias may have been a factor in these studies however and the evidence from subsequent RCTs has been negative.

Adjuvant chemotherapy in oestrogen-receptor-poor breast cancer: patient-level meta-analysis of randomised trials

Background: The long-term effects of adjuvant polychemotherapy regimens in oestrogen-receptor-poor (ER-poor) breast cancer, and the extent to which these effects are modified by age or tamoxifen use, can be assessed by an updated meta-analysis of individual patient data from randomised trials. Methods: Collaborative meta-analyses of individual patient data for about 6000 women with ER-poor breast cancer in 46 trials of polychemotherapy versus not (non-taxane-based polychemotherapy, typically about six cycles; trial start dates 1975-96, median 1984) and about 14 000 women with ER-poor breast cancer in 50 trials of tamoxifen versus not (some trials in the presence and some in the absence of polychemotherapy; trial start dates 1972-93, median 1982). Findings: In women with ER-poor breast cancer, polychemotherapy significantly reduced recurrence, breast cancer mortality, and death from any cause, in those younger than 50 years and those aged 50-69 years at entry into trials of polychemotherapy versus not. In those aged younger than 50 years (1907 women, 15% node-positive), the 10-year risks were: recurrence 33% versus 45% (ratio of 10-year risks 0·73, 2p<0·00001), breast cancer mortality 24% versus 32% (ratio 0·73, 2p=0·0002), and death from any cause 25% versus 33% (ratio 0·75, 2p=0·0003). In women aged 50-69 years (3965 women, 58% node-positive), the 10-year risks were: recurrence 42% versus 52% (ratio 0·82, 2p<0·00001), breast cancer mortality 36% versus 42% (ratio 0·86, 2p=0·0004), and death from any cause 39% versus 45% (ratio 0·87, 2p=0·0009). Few were aged 70 years or older. Tamoxifen had little effect on recurrence or death in women who were classified in these trials as having ER-poor disease, and did not significantly modify the effects of polychemotherapy. Interpretation: In women who had ER-poor breast cancer, and were either younger than 50 years or between 50 and 69 years, these older adjuvant polychemotherapy regimens were safe (ie, had little effect on mortality from causes other than breast cancer) and produced substantial and definite reductions in the 10-year risks of recurrence and death. Current and future chemotherapy regimens could well yield larger proportional reductions in breast cancer mortality.