Optimizing the generation of random amplified polymorphic DNAs in chrysanthemum

Many conditions of the RAPD reaction procedure may influence the result. This paper presents rapid detection of influential factors with a fractional factorial experiment. A more extensive study of these factors is also presented. Polymerase brand, thermal cycler brand, annealing temperature, and primer, are important factors in obtaining good DNA yields and optimal fragment patterns. Each primer has its optimal annealing temperature, and this is not correlated with the GC content of the primer. Optimal species-primer combinations have to be found by trial and error.     

不同能量CO2点阵激光对博来霉素诱导的小鼠增生性瘢痕的作用及Hedgehog信号通路的影响

目的:探讨不同能量CO_2点阵激光对博莱霉素诱导的小鼠增生性瘢痕模型的作用及其对瘢痕组织中Hedgehog信号通路的影响。方法:于雄性C57BL/6J小鼠背部皮肤注射博来霉素(1 mg/d,4周)制作增生性瘢痕模型,另取4只小鼠背部注射PBS缓冲液作为对照。造模成功之后,随机将小鼠分为瘢痕对照组(模型组),10 mj激光治疗组(10 mj组)和20 mj激光治疗组(20 mj组),每组6只小鼠。10 mj组小鼠给予10 mj激光治疗(共3次,每次间隔2周);20 mj组小鼠给予20 mj激光治疗(共3次,每次间隔2周)。治疗结束后,处死小鼠,取瘢痕全层标本进行病理组织学染色观察(HE、Masson染色)以及α-平滑肌肌动蛋白(α-SMA)、GLi1免疫荧光观察。结果:①我们成功复制出小鼠增生性瘢痕模型;②20 mj CO_2点阵激光治疗可有效修复瘢痕组织,经治疗后皮肤瘢痕程度显著减轻,同时可降低真皮层厚度和减轻瘢痕组织的纤维化程度;③免疫荧光染色结果提示,CO_2点阵激光可显著减少小鼠皮肤增生性瘢痕中α-SMA、GLi1表达。结论:于小鼠的背部皮肤注射博莱霉素可建立增生性瘢痕模型。CO_2点阵激光为治疗增生性瘢一种有效的治疗方式,其作用可能与其对Hedgehog信号通路的抑制有关。     

Nonparametric estimation for the three-stage irreversible illness-death model

In this paper, we present new nonparametric estimators of the stage-occupation probabilities in the three-stage irreversible illness-death model. These estimators use a fractional risk set and a reweighting approach and are valid under stage-dependent censoring. Using a simulated data set, we compare the behavior of our estimators with previously proposed estimators. We also apply our estimators to data on time to Pneumocystis pneumonia and death obtained from an AIDS cohort study.     

Laccase production from oil palm industry solid waste: Statistical optimization of selected process parameters

Oil palm frond parenchyma tissue was used as a solid substrate for the production of laccase via solid‐state fermentation using the white rot fungus Pycnoporus sanguineus. With a rectangular aluminium tray as solid‐state fermentation bioreactor, process parameters such as bed height, moisture and supplemented nitrogen (as urea solution) levels were studied and optimized using a statistical design of experiment. The moisture level exerted a significant effect on the process. The interaction effect observed between bed height and supplemented nitrogen level suggested that uniform distribution of supplemented nitrogen into the substrate bed was important. The proposed regression model sufficiently predicted the process response over the experimental range tested. The optimum parameter combination for laccase production was a 3‐cm bed height, 72% w/w moisture and 0.21% w/v supplemented nitrogen. Laccase productivity remained constant when the tray size was increased from 1.4 to 3.4‐fold.     

Harvesting in a random environment: Itô or Stratonovich calculus?

We extend to harvesting stochastic differential equation (SDE) models in a random environment our previous work on models without harvesting concerning the resolution of the It?-Stratonovich controversy. The resolution is obtained for the very general class of models dN/dt=N (r(N)-h(N)+sigmaepsilon(t)), where N=N(t) is the population size at time t, r(N) is the (density-dependent) "mean" per capita growth rate, h(N) is the (density-dependent) harvesting effort, epsilon(t) is a standard white noise (representing environmental random fluctuations), and sigma is a noise intensity parameter. It? and Stratonovich calculus in the resolution of SDEs apparently give different qualitative and quantitative results, leading to controversy on which calculus is more appropriate and creating an obstacle on the use of this modeling approach. We show that the apparent difference between the two calculi is due to a semantic confusion based on the fallacious assumption that we are working with the same type of mean rates. After clearing the confusion, the two calculi yield exactly the same results and we obtain important common conditions for extinction and for existence of a stationary density. The resolution of the controversy is intertwined with and sheds light on the estimation issues.     

A new proposal for multivariable modelling of time-varying effects in survival data based on fractional polynomial time-transformation

The Cox proportional hazards model has become the standard for the analysis of survival time data in cancer and other chronic diseases. In most studies, proportional hazards (PH) are assumed for covariate effects. With long-term follow-up, the PH assumption may be violated, leading to poor model fit. To accommodate non-PH effects, we introduce a new procedure, MFPT, an extension of the multivariable fractional polynomial (MFP) approach, to do the following: (1) select influential variables; (2) determine a sensible dose-response function for continuous variables; (3) investigate time-varying effects; (4) model such time-varying effects on a continuous scale. Assuming PH initially, we start with a detailed model-building step, including a search for possible non-linear functions for continuous covariates. Sometimes a variable with a strong short-term effect may appear weak or non-influential if 'averaged' over time under the PH assumption. To protect against omitting such variables, we repeat the analysis over a restricted time-interval. Any additional prognostic variables identified by this second analysis are added to create our final time-fixed multivariable model. Using a forward-selection algorithm we search for possible improvements in fit by adding time-varying covariates. The first part to create a final time-fixed model does not require the use of MFP. A model may be given from 'outside' or a different strategy may be preferred for this part. This broadens the scope of the time-varying part. To motivate and illustrate the methodology, we create prognostic models from a large database of patients with primary breast cancer. Non-linear time-fixed effects are found for progesterone receptor status and number of positive lymph nodes. Highly statistically significant time-varying effects are present for progesterone receptor status and tumour size.     

Statistical optimization of medium components for avilamycin production by <Emphasis Type="Italic">Streptomyces viridochromogenes</Emphasis> Tü57-1 using response surface methodology

A fermentation medium for avilamycin production by Streptomyces viridochromogenes Tü57-1 has been optimized. Important components and their concentrations were investigated using fractional factorial design and Box–Behnken Design. The results showed that soybean flour, soluble starch, MgSO₄·7H₂O and CaCl₂·2H₂O are important for avilamycin production. A polynomial model related to medium components and avilamycin yield had been established. A high coefficient of determination (R ² = 0.92) was obtained that indicated good agreement between the experimental and predicted values of avilamycin yield. Student’s T-test of each coefficient showed that all the linear and quadratic terms had significant effect (P > |T| < 0.05) on avilamycin yield. The significance of tested components was related to MgSO₄·7H₂O (0.37 g/L), CaCl₂·2H₂O (0.39 g/L), soybean flour (21.97 g/L) and soluble starch (37.22 g/L). The yield of avilamycin reached 88.33 ± 0.94 mg/L (p < 0.05) that was 2.8-fold the initial yield.     

Improvement of the production of a red pigment in Penicillium sp. HSD07B synthesized during co-culture with Candida tropicalis

Co-culture of Penicillium sp. HSD07B and Candida tropicalis resulted in the production of a red pigment consisting of six components as determined by TLC and HPLC. The pigment showed no acute toxicity in mice and was mot mutagenic in the Ames test. The pigment was stable between pH 2 and 10 and temperatures of 10-100 °C and exhibited good photo-stability and resistance to oxidization by hydrogen peroxide and reduction by Na₂SO₃. Glucose and ratio of C. tropicalis to strain HSD07B (w/w) in the inoculum were the important factors influencing production of the pigment. Under optimized conditions, a pigment yield of 2.75 and 7.7 g/l was obtained in a shake-flask and a 15 l bioreactor, respectively. Thus, co-culture of strain HSD07B and C. tropicalis is a promising way to produce a red pigment potentially useful for coloring applications.     

Modeling of slow glutamate diffusion and AMPA receptor activation in the cerebellar glomerulus

Synaptic conductances are influenced markedly by the geometry of the space surrounding the synapse since the transient glutamate concentration in the synaptic cleft is determined by this geometry. Our paper is an attempt to understand the reasons for slow glutamate diffusion in the cerebellar glomerulus, a structure situated around the enlarged mossy fiber terminal in the cerebellum and surrounded by a glial sheath. For this purpose, analytical expressions for glutamate diffusion in the glomerulus were considered in models with two-, three-, and fractional two-three-dimensional (2D-3D) geometry with an absorbing boundary. The time course of average glutamate concentration in the synaptic cleft of the mossy fiber-granule cell connection was calculated for both direct release of glutamate from the same synaptic unit, and for cumulative spillover of glutamate from neighboring release sites. Several kinetic schemes were examined, and the parameters of the diffusion models were estimated by identifying theoretical activation of AMPA receptors with direct release and spillover components of published experimental AMPA receptor-mediated EPSCs. For model selection, the correspondence of simulated paired-pulse ratio and EPSC increase after prevention of desensitization to experimental values were also taken into consideration. Our results suggest at least a 7- to 10-fold lower apparent diffusion coefficient of glutamate in the porous medium of the glomerulus than in water. The modeling of glutamate diffusion in the 2D-3D geometry gives the best fit of experimental EPSCs. We show that it could be only partly explained by normal diffusion of glutamate in the complex geometry of the glomerulus. We assume that anomalous diffusion of glutamate occurs in the glomerulus. A good match of experimental estimations and theoretical parameters, obtained in the simulations that use an approximation of anomalous diffusion by a solution for fractional Brownian motion, confirms our assumption.