Bayesian nonparametric inference for panel count data with an informative observation process

In this paper, the panel count data analysis for recurrent events is considered. Such analysis is useful for studying tumor or infection recurrences in both clinical trial and observational studies. A bivariate Gaussian Cox process model is proposed to jointly model the observation process and the recurrent event process. Bayesian nonparametric inference is proposed for simultaneously estimating regression parameters, bivariate frailty effects, and baseline intensity functions. Inference is done through Markov chain Monte Carlo, with fully developed computational techniques. Predictive inference is also discussed under the Bayesian setting. The proposed method is shown to be efficient via simulation studies. A clinical trial dataset on skin cancer patients is analyzed to illustrate the proposed approach.     

The strong-migration limit for the genealogical process in geographically structured populations

In this article we assume that the entire population is subdivided into a finite number of panmictic colonies, each of which consists of a respective number of haploid individuals. We also assume that random genetic drift occurs in each colony and migration among colonies, which is independent of time and ergodic. We study the genealogical process of sampled genes from geographically structured populations. We prove that if the actual total population number is replaced by the effective population number, the mean coalescence time converges to that in a panmictic population in the strong migration limit. We also obtain the geographical distribution of the common ancestor.     

An improved approach to evaluate car sharing options

We develop an improved approach to evaluate car sharing options under uncertain environments with the combination of Fuzzy Analytic Hierarchy Process (F-AHP) and Fuzzy Technique for Order Preference by Similarity to Ideal Solution (F-TOPSIS), which consists of three steps. In the first step, we propose a SCUMN (Specific, Comprehensive, Understandable, Measurable, and Neutral) methodology to identify appropriate indicators and obtain a final list of 24 indicators according to their relevance to car sharing options. In the second step, we determine the weight of each indicator with F-AHP and conduct consistency check of the comparison matrix of selected indicators. In the third step, comparison of different options is performed with selected indicators and F-TOPSIS. A case study is provided to validate the proposed approach. Twenty-four indicators are identified to evaluate five different car sharing options and rank them according to their closeness coefficients in decreasing order. And thirty-one sensitivity analysis experiments are conducted to figure out the influence of indicators on decision making. The experimental results show that the proposed approach is capable of evaluating car sharing options with uncertainty and vagueness. F-AHP is able to determine the weight for each selected indicator and F-TOPSIS demonstrates its advantage in comparing potential options.     

Esterification using a liquid lipase to remove residual free fatty acids in biodiesel

Lately, the price of liquid formulated lipase enzymes, usable in biodiesel production, has been significantly reduced. This enables one-time use of these enzymes for transesterification, and the process is used industrially. However, the process suffers a drawback by leaving 2−3 % free fatty acids in the crude biodiesel, which reduces the profitability. This article discusses a novel enzymatic FFA esterification reaction utilizing liquid lipase B from Candida antarctica (CALB) along with glycerol at low water concentrations to eliminate the residual FFA. The reaction setup was found able to reduce the free fatty acid concentration to within biodiesel specifications of < 0.25 wt.% FFA. Additionally, two alternative process setups are proposed, which were both found viable through a combination of experiments and simulations, and can be developed into full-scale processes. The resulting two-step enzymatic biodiesel process - transesterification followed by esterification - provides a potential process layout for the industrial production of biodiesel.     

Establishment of the introduced kelp Undaria pinnatifida in Tasmania depends on disturbance to native algal assemblages

Despite recent rapid increases in the occurrence of nonindigenous marine organisms in the marine environment, few studies have critically examined the invasion process for a marine species. Here we use manipulative experiments to examine processes of invasion for the Asian kelp Undaria pinnatifida (Harvey) Suringar at two sites on the east coast of Tasmania. Disturbance to reduce cover of the native algal canopy was found to be critical in the establishment of U. pinnatifida, while the presence of a stable native algal canopy inhibited invasion. In the first sporophyte growth season following disturbance of the canopy, U. pinnatifida recruited in high densities (up to 19 plants m⁻²) while remaining rare or absent in un-manipulated plots. The timing of disturbance was also important. U. pinnatifida recruited in higher densities in plots where the native canopy was removed immediately prior to the sporophyte growth season (winter 2000), compared with plots where the canopy was removed 6 months earlier during the period of spore release (spring 1999). Removal of the native canopy also resulted in a significant increase in cover of sediment on the substratum. In the second year following canopy removal, U. pinnatifida abundance declined significantly, associated with a substantial recovery of native canopy-forming species. A feature of the recovery of the native algal canopy was a significant shift in species composition. Species dominant prior to canopy removal showed little if any signs of recovery. The recovery was instead dominated by canopy-forming species that were either rare or absent in the study areas prior to manipulation of the canopy.     

Sperm cell surface characteristics of Plumbago zeylanica L. in relation to transport in the embryo sac

Myosin associated with the male germ cells of angiosperms interacts with actin, promoting transport of the non-motile generative and later sperm cells in the pollen tube. Myosin localizing on the sperm cell plasma membrane seems negligible in Plumbago, as reflected by the absence of: (i) anti-myosin labeling using immunoelectron microscopy, (ii) sperm motility on actin matrices, and (iii) electrophoretic movement changes after addition of antibody. Sperm cells injected directly into actively streaming Nitella internodal cells, however, follow actin bundles and their movement is sensitive to ATP and Mg²⁺. This may be based on simple charge binding since negatively charged latex beads also migrate on actin, whereas neutral or positively-charged latex beads do not. Sperm cells are negatively charged according to capillary microelectrophoresis, whereas killed sperm cells, which are positively charged do not migrate. The sperm cell that normally fertilizes the egg has a higher calculated charge (8.277 × 10³ esu/cm²) compared with the sperm cell that fuses with the central cell (6.120 × 10³ esu/cm²). Received: 15 December 1998 / Accepted: 21 January 1999     

SPECIATION AND FEATHER ORNAMENTATION IN BIRDS

The hypothesis that sexual selection promotes speciation has rarely been tested. We identified 70 evolutionarily independent events of feather ornaments in birds. For each focal species we noted the number of ornamented and nonornamented species belonging to its genus and its number of subspecies, as well as its mating system and the extent of its geographic range. For purposes of comparison, we randomly chose a second, nonornamented species for which we obtained information on the number of subspecies, and in cases in which the nonornamented species was in the same genus, we chose a third, nonornamented species in a related genus and obtained the same information. We then noted the number of species in each genus and the difference in numbers of species, or species richness, between paired genera. For the genera of the focal ornamented species, we regressed number of ornamented species on number of nonornamented species and found a positive relationship. As number of species per genus rose, number of ornamented species per genus rose more rapidly, indicating that more speciose genera have a higher proportion of ornamented species than less speciose genera. We then took the deviations from this regression, the residual number of species, and regressed them on the differences in species richness between the paired genera. This relationship was positive indicating that ornamented genera with more than the expected number of ornamented species were more speciose with respect to their paired genera than were genera with fewer than the expected number of ornamented species. Finally, we compared the deviations from this regression, the residual number of ornamented species, with species' mating system and found a greater residual number of ornamented species among species whose mating system is associated with greater skew in male mating success and thus more intense sexual selection. Ornamented species had more subspecies than nonornamented species, even when controlling for geographic range, suggesting an association between subspeciation and ornaments.     

Bayesian Nonparametric Modeling for Comparison of Single-Neuron Firing Intensities

Summary .  We propose a fully inferential model-based approach to the problem of comparing the firing patterns of a neuron recorded under two distinct experimental conditions. The methodology is based on nonhomogeneous Poisson process models for the firing times of each condition with flexible nonparametric mixture prior models for the corresponding intensity functions. We demonstrate posterior inferences from a global analysis, which may be used to compare the two conditions over the entire experimental time window, as well as from a pointwise analysis at selected time points to detect local deviations of firing patterns from one condition to another. We apply our method on two neurons recorded from the primary motor cortex area of a monkey's brain while performing a sequence of reaching tasks.