Synthesis and properties of defined DNA oligomers containing base mispairs involving 2-aminopurine.

DNA heptamers containing the mutagenic base analogue 2-aminopurine (AP) have been chemically synthesized and physically characterized. We report on the relative stabilities of base pairs between AP and each of the common DNA bases, as determined from heptamer duplex melts at 275 and 330 nm. Base pairs are ranked in order of decreasing stability: AP.T greater than AP.A greater than AP.C greater than AP.G. It is of interest that AP.A is more stable than AP.C even though DNA polymerase strongly favors the formation of AP.C over AP.A base pairs. Comparisons of melting profiles at 330 nm and 275 nm indicate that AP.T, AP.A, and AP.C base pairs are annealed in heptamer duplexes and melt 2-3 degrees prior to surrounding base pairs, whereas AP.G appears not to be annealed.     

Presence of a truncated M-type subunit and altered kinetic properties of 6-phosphofructo-1-kinase isozymes in the brain of a dog affected by glycogen storage disease type VII.

6-Phosphofructo-1-kinase (PFK) activity in the brain of a dog affected by glycogen storage disease type VII was only 31% of the PFK activity in the normal dog brain. PFK in the normal dog brain was composed of L-type, M-type and C-type subunits with apparent molecular weights of 78,000, 86,000, and 88,000, respectively, and subunit proportions (L:M:C) of 27:49:24. PFK in the affected dog brain was composed of nearly equal levels of the normal L-type and C-type subunits, but a normal M-type subunit was not detected. Using antidog muscle PFK IgG, immunoblots of gels containing partially purified PFK from the affected dog brain revealed a small amount of immunoreactive protein with an apparent molecular weight of 84,000, suggesting the presence of a truncated M-type subunit. Kinetic studies indicated that the PFK isozymes in the affected dog brain exhibited significantly different kinetic regulatory properties when compared to the PFK isozyme pool in the normal dog brain.     

A Flexible Alternative to the Cox Proportional Hazards Model for Assessing the Prognostic Accuracy of Hospice Patient Survival

Prognostic models are often used to estimate the length of patient survival. The Cox proportional hazards model has traditionally been applied to assess the accuracy of prognostic models. However, it may be suboptimal due to the inflexibility to model the baseline survival function and when the proportional hazards assumption is violated. The aim of this study was to use internal validation to compare the predictive power of a flexible Royston-Parmar family of survival functions with the Cox proportional hazards model. We applied the Palliative Performance Scale on a dataset of 590 hospice patients at the time of hospice admission. The retrospective data were obtained from the Lifepath Hospice and Palliative Care center in Hillsborough County, Florida, USA. The criteria used to evaluate and compare the models'' predictive performance were the explained variation statistic R², scaled Brier score, and the discrimination slope. The explained variation statistic demonstrated that overall the Royston-Parmar family of survival functions provided a better fit (R² = 0.298; 95% CI: 0.236–0.358) than the Cox model (R² = 0.156; 95% CI: 0.111–0.203). The scaled Brier scores and discrimination slopes were consistently higher under the Royston-Parmar model. Researchers involved in prognosticating patient survival are encouraged to consider the Royston-Parmar model as an alternative to Cox.     

Age-related changes in subunit composition and regulation of hepatic 6-phosphofructo-1-kinase.

6-Phosphofructo-1-kinase (PFK) isoenzyme pools from livers of fetal, neonatal, young adult (3 months) and aged (24 months) rats were studied. Near-term liver PFK isoenzyme pools were composed of nearly equal quantities of all three subunits. During the 30 days after birth, the total activity increased by 25%; the amount of the L-type, M-type or C-type subunit was increased 3-fold, was unchanged, or was decreased by 80% respectively. In aged rats, compared with young adults, total PFK activity was unchanged, but the L-type, M-type or C-type subunit decreased by 24%, increased by 39%, or increased by 338% respectively. During neonatal maturation, the changing subunit composition of the hepatic isoenzyme pools led to a decreased susceptibility to ATP inhibition, to a greater apparent affinity for fructose 6-phosphate, and to increased sensitivity to fructose 2,6-bisphosphate. Also, these alterations correlated with the measured increases in fructose 2,6-bisphosphate and the reported optimal rate of hepatic glycolysis/gluconeogenesis.     

Treatment Success in Cancer: Industry Compared to Publicly Sponsored Randomized Controlled Trials

Objective

To assess if commercially sponsored trials are associated with higher success rates than publicly-sponsored trials.

Study Design and Settings

We undertook a systematic review of all consecutive, published and unpublished phase III cancer randomized controlled trials (RCTs) conducted by GlaxoSmithKline (GSK) and the NCIC Clinical Trials Group (CTG). We included all phase III cancer RCTs assessing treatment superiority from 1980 to 2010. Three metrics were assessed to determine treatment successes: (1) the proportion of statistically significant trials favouring the experimental treatment, (2) the proportion of the trials in which new treatments were considered superior according to the investigators, and (3) quantitative synthesis of data for primary outcomes as defined in each trial.

Results

GSK conducted 40 cancer RCTs accruing 19,889 patients and CTG conducted 77 trials enrolling 33,260 patients. 42% (99%CI 24 to 60) of the results were statistically significant favouring experimental treatments in GSK compared to 25% (99%CI 13 to 37) in the CTG cohort (RR = 1.68; p = 0.04). Investigators concluded that new treatments were superior to standard treatments in 80% of GSK compared to 44% of CTG trials (RR = 1.81; p<0.001). Meta-analysis of the primary outcome indicated larger effects in GSK trials (odds ratio = 0.61 [99%CI 0.47–0.78] compared to 0.86 [0.74–1.00]; p = 0.003). However, testing for the effect of treatment over time indicated that treatment success has become comparable in the last decade.

Conclusions

While overall industry sponsorship is associated with higher success rates than publicly-sponsored trials, the difference seems to have disappeared over time.     

JAMA published fewer industry-funded studies after introducing a requirement for independent statistical analysis

Background

JAMA introduced a requirement for independent statistical analysis for industry-funded trials in July 2005. We wanted to see whether this policy affected the number of industry-funded trials published by JAMA.

Methods and Findings

We undertook a retrospective, before-and-after study of published papers. Two investigators independently extracted data from all issues of JAMA published between 1 July 2002 and 30 June 2008 (i.e., three years before and after the policy). They were not blinded to publication date. The randomized controlled trials (RCTs) were classified as industry funded (IF), joint industry/non-commercial funding (J), industry supported (IS) (when manufacturers provided materials only), non-commercial (N) or funding not stated (NS). Findings were compared and discrepancies resolved by discussion or further analysis of the reports. RCTs published in The Lancet and NEJM over the same period were used as a control group. Between July 2002 and July 2008, JAMA published 1,314 papers, of which 311 were RCTs. The number of industry studies (IF, J or IS) fell significantly after the policy (p = 0.02) especially for categories J and IS. However, over the same period, the number of industry studies rose in both The Lancet and NEJM.

Conclusions

After the requirement for independent statistical analysis for industry-funded studies, JAMA published significantly fewer RCTs and significantly fewer industry-funded RCTs. This pattern was not seen in the control journals. This suggests the JAMA policy affected the number of submissions, the acceptance rate, or both. Without analysing the submissions, we cannot check these hypotheses but, assuming the number of published papers is related to the number submitted, our findings suggest that JAMA''s policy may have resulted in a significant reduction in the number of industry-sponsored trials it received and published.