Paradigm of tunable clustering using binarization of consensus partition matrices (Bi-CoPaM) for gene discovery

Copyright @ 2013 Abu-Jamous et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Clustering analysis has a growing role in the study of co-expressed genes for gene discovery. Conventional binary and fuzzy clustering do not embrace the biological reality that some genes may be irrelevant for a problem and not be assigned to a cluster, while other genes may participate in several biological functions and should simultaneously belong to multiple clusters. Also, these algorithms cannot generate tight clusters that focus on their cores or wide clusters that overlap and contain all possibly relevant genes. In this paper, a new clustering paradigm is proposed. In this paradigm, all three eventualities of a gene being exclusively assigned to a single cluster, being assigned to multiple clusters, and being not assigned to any cluster are possible. These possibilities are realised through the primary novelty of the introduction of tunable binarization techniques. Results from multiple clustering experiments are aggregated to generate one fuzzy consensus partition matrix (CoPaM), which is then binarized to obtain the final binary partitions. This is referred to as Binarization of Consensus Partition Matrices (Bi-CoPaM). The method has been tested with a set of synthetic datasets and a set of five real yeast cell-cycle datasets. The results demonstrate its validity in generating relevant tight, wide, and complementary clusters that can meet requirements of different gene discovery studies.National Institute for Health Researc

Occurrence and distribution of tetrabromobisphenol A and its derivative in river sediments from Vaal River Catchment, South Africa

Brominated flame retardants (BFRs) compounds have been widely added in a number of products to reduce their flammability. In the present study, the concentrations and distribution of tetrabromobisphenol A (TBBPA) and its derivatives, i.e. tribromophenol dibromopropyl ether (TBPDBPE), tetrabromobisphenol A bis-dibromopropyl ether (TBBPA BDBPE), tetrabromobisphenol A bis-allyl ether (TBBPA BAE) were investigated in sediment samples collected from the Vaal River catchment, South Africa. The results showed that all these pollutants were detected in sediments with TBBPA BAE being the most abundant contaminant. The TBBPA BAE concentrations ranged from 3.5 to 44.4 ng/g (mean 16 ng/g) while the concentration ranged from not detected (nd) to 2.4 ng/g (mean 0.6 ng/g), nd - 21.0 ng/g (mean 6 ng/g) and nd - 2.0 ng/g (mean 0.2 ng/g) for TBPDBPE, TBBPA and TBBPA BDBPE; respectively. Higher concentrations of these pollutants were found in sampling sites receiving effluents of wastewater treatment works (WWTWs) treating some industrial wastewater suggesting effluents might play an important role in the contamination of BFRs in the environment. Negative correlation between TBBPA and TBBPA BAE was observed implying different sources or environmental fates between these pollutants. Overall, the results showed a need for further studies to be undertaken in investigating the presence, fate and sources of alternative halogenated flame retardants in the environment

New isoflavan from <i>Erythrina livingstoniana</i>

Chemical investigation of the root wood of Erythrina livingstoniana led to the isolation of one previously undescribed isoflavan (3S,3″R)-7-hydroxy-2′-methoxy-[3″-hydroxy-2″,2″-dimethylpyrano (3′,4′)] isoflavan 1, together with eleven known compounds 2-12. The structure of compound 1 was elucidated on the basis of extensive spectroscopic and spectrometric analyses (1 D and 2 D-NMR and APCI-HRMS), with absolute configurations established by comparison of experimental and DFT calculated ECD data. The assignment of the absolute configurations of C-3 and C-3″ of compounds 2 and 3, respectively, were reported for the first time. Compounds 1 − 4 were evaluated for their antibacterial activities in vitro against E. coli ATCC 25922 and S. aureus ATCC 25923. Compound 1 exhibited moderate antibacterial activity with MIC value of 0.063 mg/mL against the clinically relevant risk-group 2 (RG-2) bacterium S. aureus.</p