An optimal Bayesian predictive probability design for phase II clinical trials with simple and complicated endpoints

Most existing phase II clinical trial designs focus on conventional chemotherapy with binary tumor response as the endpoint. The advent of novel therapies, such as molecularly targeted agents and immunotherapy, has made the endpoint of phase II trials more complicated, often involving ordinal, nested, and coprimary endpoints. We propose a simple and flexible Bayesian optimal phase II predictive probability (OPP) design that handles binary and complex endpoints in a unified way. The Dirichlet-multinomial model is employed to accommodate different types of endpoints. At each interim, given the observed interim data, we calculate the Bayesian predictive probability of success, should the trial continue to the maximum planned sample size, and use it to make the go/no-go decision. The OPP design controls the type I error rate, maximizes power or minimizes the expected sample size, and is easy to implement, because the go/no-go decision boundaries can be enumerated and included in the protocol before the onset of the trial. Simulation studies show that the OPP design has satisfactory operating characteristics.     

An alternative route for the folding of large RNAs: apparent two-state folding by a group II intron ribozyme

Despite a growing literature on the folding of RNA, our understanding of tertiary folding in large RNAs derives from studies on a small set of molecular examples, with primary focus on group I introns and RNase P RNA. To broaden the scope of RNA folding models and to better understand group II intron function, we have examined the tertiary folding of a ribozyme (D135) that is derived from the self-splicing ai5gamma intron from yeast mitochondria. The D135 ribozyme folds homogeneously and cooperatively into a compact, well-defined tertiary structure that includes all regions critical for active-site organization and substrate recognition. When D135 was treated with increasing concentrations of Mg(2+) and then subjected to hydroxyl radical footprinting, similar Mg(2+) dependencies were seen for internalization of all regions of the molecule, suggesting a highly cooperative folding behavior. In this work, we show that global folding and compaction of the molecule have the same magnesium dependence as the local folding previously observed. Furthermore, urea denaturation studies indicate highly cooperative unfolding of the ribozyme that is governed by thermodynamic parameters similar to those for forward folding. In fact, D135 folds homogeneously and cooperatively from the unfolded state to its native, active structure, thereby demonstrating functional reversibility in RNA folding. Taken together, the data are consistent with two-state folding of the D135 ribozyme, which is surprising given the size and multi-domain structure of the RNA. The findings establish that the accumulation of stable intermediates prior to formation of the native state is not a universal feature of RNA folding and that there is an alternative paradigm in which the folding landscape is relatively smooth, lacking rugged features that obstruct folding to the native state.     

An alternative approach for evaluating the phenotypic virulence factors of pathogenic Escherichia coli

Escherichia coli is a recognized zoonotic food-borne pathogen; however, the use of polymerase chain reaction (PCR) in the underdeveloped countries to differentiate pathogenic from non-pathogenic E. coli is a problematic issue. Our grail was to assess the phenotypic virulence markers motility, hemolysin, congo red agar, embryo lethality assay and serum resistance for pathogenic E. coli (PEC) correlated to PCR tests which is currently used world-wide to evaluate the PEC. The 448 strains of Escherichia coli that were isolated from different sources, were characterized for phenotypic virulence factors such as motility, hemolysin, Congo red binding, Embryo Lethality assay (ELA) and serum resistance, as well as antibiotic susceptibility using disc diffusion method to 23 antibiotics. Results exhibited 100% motility and Congo red binding, 97.1% for hemolysin production and 90.2% in the ELA. As a result, we were able to hypothetically conclude that the aforementioned virulence markers are plain, straightforward, economical, rapid, more dynamic, uncomplicated methodology, duplicatable and cost next to nothing when compared to the molecular PCR. Their implementation in a diagnostic microbiology laboratory for vetting is a rewarding task in the underdeveloped countries. It augments endeavors to minimize the use of PCR in our investigations especially during epidemiological and outbreak investigations of PEC.     

A comparison of alternative sample preparation procedures for the analysis of swainsonine using LC‐MS/MS

Introduction – Swainsonine, a polyhydroxy indolizidine alkaloid and known glycosidase inhibitor, is found in a number of different plants that cause a lysosomal storage disease known as locoism in the western USA. Most recently swainsonine has been analysed by LC‐MS/MS after sample extraction and preparation from ion‐exchange resins. Objective – To compare previously published sample preparation procedures with several new alternative procedures to provide methods using either commercially available solid‐phase extraction equipment or procedures which significantly reduce sample preparation time. Methodology – A previously reported and validated sample preparation method using ion‐exchange resin was compared with methods using a commercially available solid‐phase extraction cartridge, a solvent partitioning procedure or a single solvent extraction procedure using one of two solvents. Twenty different plant samples of varying swainsonine concentrations were prepared in triplicate and analysed by LC‐MS/MS. The measured concentration of swainsonine was then statistically compared between methods. Results – There were no statistically significant differences found between four of the five different sample preparation methods tested. Conclusion – A commercially available SPE cartridge can be used to replace the previously used ion‐exchange resin for swainsonine analysis. For very rapid analyses the SPE procedure can be eliminated and a simple, single solvent extraction step used for sample preparation. Published in 2010 by John Wiley & Sons, Ltd.     

An RNA foldability metric; implications for the design of rapidly foldable RNA sequences

Evidence is presented suggesting, for the first time, that the protein foldability metric σ = (T_θ − T_f) / T_θ, where T_θ and T_f are, respectively, the collapse and folding transition temperatures, could be used also to measure the foldability of RNA sequences. These results provide further evidence of similarities between the folding energy landscapes of proteins and RNA. The importance of σ is discussed in the context of the in silico design of rapidly foldable RNA sequences.     

An energy budget approach for evaluating the biocontrol potential of cotton aphid (Aphis gossypii) by the ladybeetle Propylaea japonica

Biological control of economically important crop pests is an important component of integrated pest management (IPM) strategies. Predator–prey energy relationships are critical to the success of biocontrol strategies; however, these relationships are often ignored in many IPM programs. In this study, the biocontrol potential of cotton aphid, Aphis gossypii (Glover) (Hemiptera: Aphididae), by the ladybeetle Propylaea japonica (Thunberg) (Coleoptera: Coccinellidae) was estimated in terms of energy budgets calculated at 27 ± 1 °C. The energy equivalent of prey subjects (aphids) consumed was estimated from bomb calorimetry and partitioned into the energy associated with ingestion, assimilation, respiration, reproduction, and waste for each developmental stage of the lady beetle. The average assimilation efficiencies for larval and adult ladybeetles were 88.2 and 91.1%, respectively, whereas net ecological efficiencies were 17.6% for larvae and 2.6% for adults. Similarly, assimilation efficiencies of cotton aphids were 71.5 and 74.4% for nymphs and adults, respectively. Based on energy budget calculations, approximately 520, 3‐day‐old aphids and 5 356, 3‐day‐old aphids were estimated to be consumed by the ladybeetle larval stage and the female adult stage, respectively. These estimates were similar to the actual number of aphids consumed by the ladybeetles, based on actual counts. The current data demonstrate that P. japonica is an important natural enemy of the cotton aphid, and that predator–prey energy relationships can play a critical role in biocontrol strategies and IPM programs.     

Mixture design as a potential tool in modeling the effect of light wavelength on Dunaliella salina cultivation: an alternative solution to increase microalgae lipid productivity for biodiesel production

Abstract

For a feasible microalgae biodiesel, increasing lipid productivity is a key parameter. An important cultivation parameter is light wavelength (λ). It can affect microalgal growth, lipid yield, and fatty acid composition. In the current study, the mixture design was used as an alternative to model the influence of the λ on the Dunaliella salina lipid productivity. The illumination was considered to be the mixture of different λ (the light colors blue, red, and green). All experiments were performed with and without sodium acetate (4?g/L), as carbon source, allowing the identification of the impact of the cultivation regimen (autotrophic or mixotrophic). Without sodium acetate, the highest lipid productivity was obtained using blue and red light. The use of mixotrophic cultivations significantly enhanced the results. The optimum obtained result was mixotrophic cultivation under 65% blue and 35% green light, resulting in biomass productivity of 105.06 mgL^?1day^?1, a lipid productivity of 53.47 mgL^?1day^?1, and lipid content of 50.89%. The main fatty acids of the oil obtained in this cultivation were oleic acid (36.52%) and palmitic acid (18.31%).