Binomial confidence intervals for testing non-inferiority or superiority: a practitioner's dilemma.

In testing for non-inferiority or superiority in a single arm study, the confidence interval of a single binomial proportion is frequently used. A number of such intervals are proposed in the literature and implemented in standard software packages. Unfortunately, use of different intervals leads to conflicting conclusions. Practitioners thus face a serious dilemma in deciding which one to depend on. Is there a way to resolve this dilemma? We address this question by investigating the performances of ten commonly used intervals of a single binomial proportion, in the light of two criteria, viz., coverage and expected length of the interval.

Weighted profile likelihood-based confidence interval for the difference between two proportions with paired binomial data.

Inference on the difference between two binomial proportions in the paired binomial setting is often an important problem in many biomedical investigations. Tang et al. (2010, Statistics in Medicine) discussed six methods to construct confidence intervals (henceforth, we abbreviate it as CI) for the difference between two proportions in paired binomial setting using method of variance estimates recovery. In this article, we propose weighted profile likelihood-based CIs for the difference between proportions of a paired binomial distribution. However, instead of the usual likelihood, we use weighted likelihood that is essentially making adjustments to the cell frequencies of a 2 × 2 table in the spirit of Agresti and Min (2005, Statistics in Medicine). We then conduct numerical studies to compare the performances of the proposed CIs with that of Tang et al. and Agresti and Min in terms of coverage probabilities and expected lengths. Our numerical study clearly indicates that the weighted profile likelihood-based intervals and Jeffreys interval (cf. Tang et al.) are superior in terms of achieving the nominal level, and in terms of expected lengths, they are competitive. Finally, we illustrate the use of the proposed CIs with real-life examples.

A novel drug eluting ureteral stent: a prospective, randomized, multicenter clinical trial to evaluate the safety and effectiveness of a ketorolac loaded ureteral stent.

PURPOSE: We evaluated the short-term safety and efficacy of a ketorolac loaded ureteral stent compared to a standard stent (control). MATERIALS AND METHODS: In this prospective, multicenter, double-blind study patients were randomized 1:1 to ketorolac loaded or control stents after ureteroscopy. The primary end point was an intervention for pain defined as unscheduled physician contact, change in pain medication or early stent removal. Secondary end points included medication use and pain visual analog score. A total of 20 patients underwent serum safety testing for ketorolac levels. RESULTS: None of the safety cohort had detectable serum ketorolac levels. Among the 276 patients there was no difference in primary (9.0% ketorolac loaded vs 7.0% control, p = 0.66) or secondary (22.6% ketorolac loaded vs 25.2% control, p = 0.67) intervention rates. Mean pain pill count at day 3 was lower in the ketorolac loaded stent group than in the control group (p <0.05). A higher number (p = 0.057) of patients with ketorolac loaded (32%) stents used no or limited pain medications compared to controls (22%). A higher number of male patients with ketorolac loaded stents used no pain medication on days 3 and 4 compared to female patients with ketorolac loaded stents, and male and female control patients (p <0.05). CONCLUSIONS: The overall safety of the ketorolac loaded stent was confirmed. Although there was no significant difference in primary or secondary intervention rates, a trend toward a treatment benefit was noted for patients receiving drug loaded stents. Specifically young male patients appeared to require less pain medication when the ketorolac loaded stent was used. Future studies with higher drug concentrations or alternative drug eluting stents may prove beneficial.

Measurement of helium isotopes in soil gas as an indicator of tritium groundwater contamination.

The focus of this study was to define the shape and extent of tritium groundwater contamination emanating from a legacy burial ground and to identify vadose zone sources of tritium using helium isotopes (3He and 4He) in soil gas. Helium isotopes were measured in soil-gas samples collected from 70 sampling points around the perimeter and downgradient of a burial ground that contains buried radioactive solid waste. The soil-gas samples were analyzed for helium isotopes using rare gas mass spectrometry. 3He/4He ratios, reported as normalized to the air ratio (RA), were used to locate the tritium groundwater plume emanating from the burial ground. The 3He (excess) suggested that the general location of the tritium source is within the burial ground. This study clearly demonstrated the efficacy of the 3He method for application to similar sites elsewhere within the DOE weapons complex.

Dissecting the catalytic mechanism of betaine-homocysteine S-methyltransferase by use of intrinsic tryptophan fluorescence and site-directed mutagenesis.

Betaine-homocysteine S-methyltransferase (BHMT) is a zinc-dependent enzyme that catalyzes the transfer of a methyl group from glycine betaine (Bet) to homocysteine (Hcy) to form dimethylglycine (DMG) and methionine (Met). Previous studies in other laboratories have indicated that catalysis proceeds through the formation of a ternary complex, with a transition state mimicked by the inhibitor S-(delta-carboxybutyl)-l-homocysteine (CBHcy). Using changes in intrinsic tryptophan fluorescence to determine the affinity of human BHMT for substrates, products, or CBHcy, we now demonstrate that the enzyme-substrate complex reaches its transition state through an ordered bi-bi mechanism in which Hcy is the first substrate to bind and Met is the last product released. Hcy, Met, and CBHcy bind to the enzyme to form binary complexes with K(d) values of 7.9, 6.9, and 0.28 microM, respectively. Binary complexes with Bet and DMG cannot be detected with fluorescence as a probe, but Bet and DMG bind tightly to BHMT-Hcy to form ternary complexes with K(d) values of 1.1 and 0.73 microM, respectively. Mutation of each of the seven tryptophan residues in human BHMT provides evidence that the enzyme undergoes two distinct conformational changes that are reflected in the fluorescence of the enzyme. The first is induced when Hcy binds, and the second, when Bet binds. As predicted by the crystal structure of BHMT, the amino acids Trp44 and Tyr160 are involved in binding Bet, and Glu159 in binding Hcy. Replacing these residues by site-directed mutagenesis significantly reduces the catalytic efficiency (V(max)/K(m)) of the enzyme. Replacing Tyr77 with Phe abolishes enzyme activity.

Structures of the N-terminal modules imply large domain motions during catalysis by methionine synthase.

B(12)-dependent methionine synthase (MetH) is a large modular enzyme that utilizes the cobalamin cofactor as a methyl donor or acceptor in three separate reactions. Each methyl transfer occurs at a different substrate-binding domain and requires a different arrangement of modules. In the catalytic cycle, the cobalamin-binding domain carries methylcobalamin to the homocysteine (Hcy) domain to form methionine and returns cob(I)alamin to the folate (Fol) domain for remethylation by methyltetrahydrofolate (CH(3)-H(4)folate). Here, we describe crystal structures of a fragment of MetH from Thermotoga maritima comprising the domains that bind Hcy and CH(3)-H(4)folate. These substrate-binding domains are (beta alpha)(8) barrels packed tightly against one another with their barrel axes perpendicular. The properties of the domain interface suggest that the two barrels remain associated during catalysis. The Hcy and CH(3)-H(4)folate substrates are bound at the C termini of their respective barrels in orientations that position them for reaction with cobalamin, but the two active sites are separated by approximately 50 A. To complete the catalytic cycle, the cobalamin-binding domain must travel back and forth between these distant active sites.

Betaine-homocysteine methyltransferase: zinc in a distorted barrel.

Betaine-homocysteine methyl transferase (BHMT) catalyzes the synthesis of methionine from betaine and homocysteine (Hcy), utilizing a zinc ion to activate Hcy. BHMT is a key liver enzyme that is important for homocysteine homeostasis. X-ray structures of human BHMT in its oxidized (Zn-free) and reduced (Zn-replete) forms, the latter in complex with the bisubstrate analog, S(delta-carboxybutyl)-L-homocysteine, were determined at resolutions of 2.15 A and 2.05 A. BHMT is a (beta/alpha)(8) barrel that is distorted to construct the substrate and metal binding sites. The zinc binding sequences G-V/L-N-C and G-G-C-C are at the C termini of strands beta6 and beta8. Oxidation to the Cys217-Cys299 disulfide and expulsion of Zn are accompanied by local rearrangements. The structures identify Hcy binding fingerprints and provide a prototype for the homocysteine S-methyltransferase family.

Representative Sampling of High-Level Radioactive Waste Tank Headspaces.

Headspaces of the underground high-level radioactive waste-storage tanks at the U.S. Department of Energy's Hanford Site have been sampled to resolve tank safety and industrial hygiene issues and to estimate regulated air pollutant emissions. Because sampling these tanks is difficult and expensive, samples have been collected from a single location of the headspaces, based on the supposition that this would provide representative samples. In most tanks, mixing of vapors occurs because of thermally driven convection from heat generated by radioactive decay of the waste. However, in some low-temperature tanks, the ground temperature above the tank may be warmer than the waste, minimizing thermally induced convection, and raising the concern that samples from a single location may not be representative. To resolve this issue, six samples at different vertical and horizontal locations were taken from each of three low-temperature tanks and analyzed for ammonia, water, permanent gases, total non-methane organic compound concentration, and selected organic vapors. Statistical analysis of the data indicated that the tanks did not exhibit significant horizontal or vertical concentration gradients.