Tree-Structured Stick Breaking Processes for Hierarchical Data

Many data are naturally modeled by an unobserved hierarchical structure. In this paper we propose a flexible nonparametric prior over unknown data hierarchies. The approach uses nested stick-breaking processes to allow for trees of unbounded width and depth, where data can live at any node and are infinitely exchangeable. One can view our model as providing infinite mixtures where the components have a dependency structure corresponding to an evolutionary diffusion down a tree. By using a stick-breaking approach, we can apply Markov chain Monte Carlo methods based on slice sampling to perform Bayesian inference and simulate from the posterior distribution on trees. We apply our method to hierarchical clustering of images and topic modeling of text data.

Comparative molecular cytogenetic studies in the order Carnivora: mapping chromosomal rearrangements onto the phylogenetic tree

We have made a set of chromosome-specific painting probes for the American mink by degenerate oligonucleotide primed-PCR (DOP-PCR) amplification of flow-sorted chromosomes. The painting probes were used to delimit homologous chromosomal segments among human, red fox, dog, cat and eight species of the family Mustelidae, including the European mink, steppe and forest polecats, least weasel, mountain weasel, Japanese sable, striped polecat, and badger. Based on the results of chromosome painting and G-banding, comparative maps between these species have been established. The integrated map demonstrates a high level of karyotype conservation among mustelid species. Comparative analysis of the conserved chromosomal segments among mustelids and outgroup species revealed 18 putative ancestral autosomal segments that probably represent the ancestral chromosomes, or chromosome arms, in the karyotype of the most recent ancestor of the family Mustelidae. The proposed 2n = 38 ancestral Mustelidae karyotype appears to have been retained in some modern mustelids, e.g., Martes, Lutra, ktonyx, and Vormela. The derivation of the mustelid karyotypes from the putative ancestral state resulted from centric fusions, fissions, the addition of heterochromatic arms, and occasional pericentric inversions. Our results confirm many of the evolutionary conclusions suggested by other data and strengthen the topology of the carnivore phylogenetic tree through the inclusion of genome-wide chromosome rearrangements. Copyright (C) 2002 S. KargerAG, Basel.

Water quality parameters of coastal shrimp farms from southwest and southeast regions of Bangladesh

The impacts of shrimp farming on water quality and effluent loading of shrimp farms in southwest (Khulna) and southeast (Cox's Bazar) regions of Bangladesh was investigated during March-August and August-October season, respectively. Water salinity fluctuated from 3.0 to 15.0 ppt in the southwest, whereas it was between 2.5 to 20.0 ppt. in southeast region. Total ammonia nitrogen as recorded in most farms of Cox's Bazar region was higher (0. 1160.438 mg/L) than the recommended level of shrimp farming. Mean values of total ammonia nitrogen and total nitrogen at the outlet of shrimp farms were higher than those of inlet in both regions. Mean values of phosphate phosphorus and total phosphorus at outlet were lower than inlet except in harvest time of Penaeus monodon. Total suspended solids were deposited on the bottom of shrimp farms in both regions, which resulted in higher concentration in inlets than outlets in both regions.

Observation on some of the environmental parameters of selected shrimp farms in Khulna, Bangladesh

In recent years, the ecological degradation, loss of technological sustenance and other multidimensional consequences caused by shrimp farming have made the experts and authorities bound to rethink about the development of the industry. The present study describes the water and sediment quality, and culture and management techniques in five selected shrimp farms at Paikgacha, Khulna throughout a production cycle from March to September 1997. The water quality parameters were found to be more or less suitable throughout the cycle. The concentration of the limiting major nutrients such as nitrogen and phosphorus and minor nutrients such as calcium and magnesium were satisfactorily high, concentrations of the organic matter content were also high. Remarkable negative correlation of shrimp production with secchi depth was observed among the farms. Production per cycle ranged between 273 kg/ha and as low as 63 kg/ha.