Simultaneous group sequential analysis of rank-based and weighted Kaplan-Meier tests for paired censored survival data

This research sequentially monitors paired survival differences using a new class of nonparametric tests based on functionals of standardized paired weighted log-rank (PWLR) and standardized paired weighted Kaplan-Meier (PWKM) tests. During a trial, these tests may alternately assume the role of the more extreme statistic. By monitoring PEMAX, the maximum between the absolute values of the standardized PWLR and PWKM, one combines advantages of rank-based (RB) and non-RB paired testing paradigms. Simulations show that monitoring treatment differences using PEMAX maintains type I error and is nearly as powerful as using the more advantageous of the two tests in proportional hazards (PH) as well as non-PH situations. Hence, PEMAX preserves power more robustly than individually monitored PWLR and PWKM, while maintaining a reasonably simple approach to design and analysis of results. An example from the Early Treatment Diabetic Retinopathy Study (ETDRS) is given.     

Optimal conditional error functions for the control of conditional power

Ethical considerations and the competitive environment of clinical trials usually require that any given trial have sufficient power to detect a treatment advance. If at an interim analysis the available data are used to decide whether the trial is promising enough to be continued, investigators and sponsors often wish to have a high conditional power, which is the probability to reject the null hypothesis given the interim data and the alternative of interest. Under this requirement a design with interim sample size recalculation, which keeps the overall and conditional power at a prespecified value and preserves the overall type I error rate, is a reasonable alternative to a classical group sequential design, in which the conditional power is often too small. In this article two-stage designs with control of overall and conditional power are constructed that minimize the expected sample size, either for a simple point alternative or for a random mixture of alternatives given by a prior density for the efficacy parameter. The presented optimality result applies to trials with and without an interim hypothesis test; in addition, one can account for constraints such as a minimal sample size for the second stage. The optimal designs will be illustrated with an example, and will be compared to the frequently considered method of using the conditional type I error level of a group sequential design.     

Linear and bent oxo-bridged dinuclear rhenium(V) complexes with terminal and bridging pyrazole ligands

The [ReOX₃(AsPh₃)(OAsPh₃)] (X = Cl or Br) complexes react with two equivalents of 3,5-dimetylopyrazole (3,5-Me₂pzH) in acetone at room temperature to give [{Re(O)X₂(3,5- Me₂pzH)₂}₂(μ-O)] (1 and 2). In the case of [ReOBr₃(AsPh₃)(OAsPh₃)], a small quantity of the dinuclear rhenium complex [{Re(O)Br(3,5-Me₂pzH)}₂(μ-O)(μ-3,5-Me₂pz)₂] (3) has been isolated next to the main product 2. Treatment of [ReOX₃(PPh₃)₂] compounds with two equivalents of 3,5-Me₂pzH in acetone at room temperature leads to the isolation of symmetrically substituted dinuclear rhenium complexes [{Re(O)X(PPh₃)}₂(μ-O)(μ-3,5-Me₂pz)₂] (4 and 5). Refluxing of [ReO(OEt)X₂(PPh₃)₂] complexes with 3,5-Me₂pzH in ethanol affords unsymmetrically substituted dinuclear rhenium [{Re(O)X(PPh₃)}(μ-O)(μ-3,5-Me₂pz)₂{Re(O)X(3,5- Me₂pzH)}] complexes (6 and 7). The complexes obtained in these reactions have been characterised by IR, UV-Vis, ¹H and ³¹P NMR. The crystal and molecular structures have been determined for 1, 2, 3, 4, 6 and 7 complexes.     

Possible processes releasing nonexchangeable potassium from the rhizosphere of maize

The source and the releasing processes of nonexchangeable K from the rhizosphere were evaluated by using a 0.01 M HCl sequential extraction that enables the detection of subtle depletion of nonexchangeable K in the rhizosphere. Rhizobox experiments were conducted in which maize (Zea mays L.) plants were grown on different K sources (non-allophanic Andosol, Fluvisol, biotite and orthoclase) for 17 days. Nonexchangeable K decreased significantly in the rhizosphere of Andosol, Fluvisol and biotite, but not of orthoclase. The width of depletion was about 0–1 mm from the root-accumulating compartment regardless of the K sources, and was much less than that of exchangeable (5–10 mm) and water-soluble (50 mm) K. Rhizosphere pHs were above 4.5 in any treatment. These results suggested that the main source of nonexchangeable K for maize was interlayer K in 2:1 type phyllosilicate, and that the releasing process involved was cation exchange of the K rather than mineral dissolution by protons. For the exchange of interlayer K, a decrease of solution K⁺ below a certain threshold is known as a prerequisite. But the concentration of solution K⁺ at the root compartment of Andosol or Fluvisol, estimated to be more than 100 M, was relatively higher than the known thresholds. Moreover, the significant release of nonexchangeable K from biotite occurred only at the root compartment where marked depletion of solution K⁺ was not observed. We therefore suggest that the release of interlayer K from the rhizosphere can occur even without a marked depletion of solution K⁺ through the following processes; (1) accumulation of cations such as Ca²⁺, Mg²⁺ or Na⁺ in the rhizosphere, (2) their adsorption on 2:1 type clay minerals near the edge of interlayer but inaccessible and nonexchangeable by NH₄ ⁺, (3) concomitant removal of the NH₄ ⁺-nonexchangable K even above the known thresholds of solution K⁺, which is followed by the expansion of the interlayer space, and (4) further removal of the deeper K by repetition of the above processes.     

Isolation and characterization of anti-Salmonella lactic acid bacteria from the porcine gastrointestinal tract

AIMS: To identify lactic acid bacteria (LAB) of porcine intestinal origin with anti-Salmonella activity. METHODS AND RESULTS: Samples were obtained from pig faeces and caeca and screened for the presence of anti-Salmonella LAB. The 11 most promising isolates were identified as belonging to the genera Lactobacillus and Pediococcus. The LAB exhibited large variation in their ability to survive in simulated gastric juice at pH 1.85. While Lactobacillus johnsonii species survived at levels of 80% for up to 30 min, Lactobacillus pentosus species declined to <0.001% in that time. All isolates tolerated porcine bile at a concentration of 0.3% (w/v), with some isolates capable of growth in the presence of up to 5% (w/v) bile. The ability of the LAB isolates to prevent Salmonella invasion of intestinal epithelial HT-29 cells varied, with reductions of between 30% (Lact. pentosus) and 80% (Lactobacillus murinus spp.) observed. CONCLUSIONS: LAB of porcine origin were observed to survive simulated passage through the GIT and inhibit growth of Salmonella and its invasion of the intestinal epithelium. SIGNIFICANCE AND IMPACT OF THE STUDY: The data demonstrate that some porcine intestinal LAB isolates may offer potential as probiotics for the reduction of Salmonella carriage in pigs.     

A scalable, GFP-based pipeline for membrane protein overexpression screening and purification

We describe a generic, GFP-based pipeline for membrane protein overexpression and purification in Escherichia coli. We exemplify the use of the pipeline by the identification and characterization of E. coli YedZ, a new, membrane-integral flavocytochrome. The approach is scalable and suitable for high-throughput applications. The GFP-based pipeline will facilitate the characterization of the E. coli membrane proteome and serves as an important reference for the characterization of other membrane proteomes.     

SSF production,purification and characterization of chitin deacetylase from Aspergillus flavus

The production of an extracellular chitin deacetylase (CDA) produced by Aspergillus flavus under solid-substrate fermentation (SSF) using wheat bran as substrate was optimized using statistical methods. The CDA production in SSF increased 1.79-fold in comparison to the unoptimized basal level medium. It was purified to a final purity of 3.94-fold by ammonium sulphate precipitation, ion-exchange chromatography, and gel-permeation chromatography (GPC) consecutively and further characterized. The molecular mass of the enzyme was estimated to be about 28?kDa by sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) and GPC analysis. The optimum pH and temperature of the purified enzyme were pH 8.0 and 50?°C, respectively. Additionally, the effect of some cations and other chemical compounds on the CDA activity was studied. A marginal increase in enzyme activity was observed with metal ions mainly Mn²⁺ and Zn²⁺. No inhibition of the enzyme was observed by the end product, that is, acetate up to 70?mM concentration. The K_m and k_cat values of the enzyme were determined to be 9.45?mg mL^?1 and 26.72?s^?1 respectively, using colloidal chitin as substrate. Among various substrates tested, glycol chitin and colloidal chitin were deacetylated.     

Optimization and production of curdlan gum using Bacillus cereus PR3 isolated from rhizosphere of leguminous plant

Curdlan gum is a neutral water-insoluble bacterial exopolysaccharide composed primarily of linear β-(1,3) glycosidic linkages. Recently, there has been increasing interest in the applications of curdlan and its derivatives. Curdlan is found to inhibit tumors and its sulfated derivative possess anti-HIV activity. Curdlan is biodegradable, non-toxic towards human, environment and edible which makes it suitable as drug-delivery vehicles for sustained drug release. The increasing demand for the growing applications of curdlan requires an efficient high yield fermentation production process so as to satisfy the industrial needs. In this perspective, the present work is aimed to screen and isolate an efficient curdlan gum producing bacteria from rhizosphere of ground nut plant using aniline-blue agar. High yielding isolate was selected based on curdlan yield and identified as Bacillus cereus using gas-chromatography fatty acid methyl ester analysis. B. cereus PR3 curdlan gum was characterized using FT-IR spectroscopy, SEM, XRD and TGA. Fermentation time for curdlan production using B. cereus PR3 was optimized. Media constituents like carbon, nitrogen and mineral sources were screened using Plackett–Burman design. Subsequent statistical analysis revealed that Starch, NH₄NO₃, K₂HPO₄, Na₂SO₄, KH₂SO₄ and CaCl₂ were significant media constituents and these concentrations were optimized for enhancement of curdlan production up to 20.88?g/l.     

Characterization of a novel alkaline esterase from Altererythrobacter epoxidivorans CGMCC 1.7731T

A novel esterase gene (e25) was identified from Altererythrobacter epoxidivorans CGMCC 1.7731^T by genome sequence screening. The e25 gene is 948 nucleotides in length and encodes a 315?amino acid protein (E25) with a predicted molecular mass of 33,683 Da. A phylogenetic tree revealed that E25 belongs to the hormone-sensitive lipase (HSL) family of lipolytic enzymes. An activity assay of E25 showed that it exhibited the highest catalytic efficiency when using p-nitrophenyl caproate (C6) as a substrate. The optimum pH and temperature were determined to be approximately pH 9 and 45°C, and the K_m and V_max values were 0.12?mM and 1,772?µmol/min/mg, respectively. After an incubation at 40°C for 80?min, E25 retained 75% of its basal activity. The enzyme exhibited good tolerance to metal cations, such as Ba²⁺, Ca²⁺, and Cu²⁺ (10?mM), but its activity was strongly inhibited by Co²⁺, Ni²⁺, Mn²⁺, and Zn²⁺. The E25 enzyme was stimulated by glycerol and retained over 60% of its basal activity in the presence of 1% Tween-80 and Triton X-100. Overall, the activity of E25 under alkaline conditions and its organic solvent and detergent tolerance indicate that E25 could be useful as a novel industrial catalyst in biotechnological applications.     

Commonly Occurring Cell Subsets in High-Grade Serous Ovarian Tumors Identified by Single-Cell Mass Cytometry

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