Influence of Matrices on Oxygen Sensing of Three Sensing Films with Chemically Conjugated Platinum Porphyrin Probes and Preliminary Application for Monitoring of Oxygen Consumption of Escherichia coli (E. coli)

Oxygen sensing films were synthesized by a chemical conjugation of functional platinum porphyrin probes in silica gel, polystyrene (PS), and poly(2-hydroxyethyl methacrylate) (PHEMA) matrices. Responses of the sensing films to gaseous oxygen and dissolved oxygen were studied and the influence of the matrices on the sensing behaviors was investigated. Silica gel films had the highest fluorescence intensity ratio from deoxygenated to oxygenated environments and the fastest response time to oxygen. PHEMA films had no response to gaseous oxygen, but had greater sensitivity and a faster response time for dissolved oxygen than those of PS films. The influence of matrices on oxygen response, sensitivity and response time was discussed. The influence is most likely attributed to the oxygen diffusion abilities of the matrices. Since the probes were chemically immobilized in the matrices, no leaching of the probes was observed from the sensing films when applied in aqueous environment. One sensing film made from the PHEMA matrix was used to preliminarily monitor the oxygen consumption of Escherichia coli (E. coli) bacteria. E. coli cell density and antibiotics ampicillin concentration dependent oxygen consumption was observed, indicating the potential application of the oxygen sensing film for biological application.     

A rapid computational filter for predicting the rate of human renal clearance

In silico models that predict the rate of human renal clearance for a diverse set of drugs, that exhibit both active secretion and net re-absorption, have been produced using three statistical approaches. Partial Least Squares (PLS) and Random Forests (RF) have been used to produce continuous models whereas Classification And Regression Trees (CART) has only been used for a classification model. The best models generated from either PLS or RF produce significant models that can predict acids/zwitterions, bases and neutrals with approximate average fold errors of 3, 3 and 4, respectively, for an independent test set that covers oral drug-like property space. These models contain additional information on top of any influence arising from plasma protein binding on the rate of renal clearance. Classification And Regression Trees (CART) has been used to generate a classification tree leading to a simple set of Renal Clearance Rules (RCR) that can be applied to man. The rules are influenced by lipophilicity and ion class and can correctly predict 60% of an independent test set. These percentages increase to 71% and 79% for drugs with renal clearances of < 0.1 ml/min/kg and > 1 ml/min/kg, respectively. As far as the authors are aware these are the first set of models to appear in the literature that predict the rate of human renal clearance and can be used to manipulate molecular properties leading to new drugs that are less likely to fail due to renal clearance.     

Asymmetric information distances for automated taxonomy construction

A novel method for automatically constructing taxonomies for specific research domains is presented. The proposed methodology uses term co-occurrence frequencies as an indicator of the semantic closeness between terms. To support the automated creation of taxonomies or subject classifications we present a simple modification to the basic distance measure, and describe a set of procedures by which these measures may be converted into estimates of the desired taxonomy. To demonstrate the viability of this approach, a pilot study on renewable energy technologies is conducted, where the proposed method is used to construct a hierarchy of terms related to alternative energy. These techniques have many potential applications, but one activity in which we are particularly interested is the mapping and subsequent prediction of future developments in the technology and research.     

Assessing tropical cyclone impacts using object-based moderate spatial resolution image analysis: a case study in Bangladesh

The environmental and societal impacts of tropical cyclones could be reduced using a range of management initiatives. Remote sensing can be a cost effective, accurate, and potential tool for mapping the multiple impacts caused by tropical cyclones using high-to-moderate spatial resolution (5–30 m) satellite imagery to provide data on the following essential parameters – evacuation, relief, and management of natural resources. This study developed and evaluated an approach for assessing the impacts of tropical cyclones through object-based image analysis and moderate spatial resolution imagery. Pre- and post-cyclone maps of artificial and natural features are required for assessing the overall impacts in the landscape that could be acquired by mapping specific land cover types. We used the object-based approach to map land-cover types in pre- and post-cyclone Satellite Pour l’Observation de la Terre (SPOT) 5 image data and the post-classification comparison technique to identify changes in the particular features in the landscape. Cyclone Sidr (2007) was used to test the applicability of this approach in Sarankhola Upazila in Bangladesh. The object-based approach provided accurate results for classifying features from pre- and post-cyclone satellite images with an overall accuracy of 95.43% and 93.27%, respectively. Mapped changes identified the extent, type, and form of cyclone induced impacts. Our results indicate that 63.15% of the study area was significantly affected by cyclone Sidr. The majority of mapped damage was found in vegetation, cropped lands, settlements, and infrastructure. The damage results were verified through the high spatial resolution satellite imagery, reports and pictures that were taken after the cyclone. The methods developed may be used in future to assess the multiple impacts caused by tropical cyclones in Bangladesh and other similar environments for the purposes of tropical cyclone disaster management.     

Interactive visualization and analysis of transitional flow

A stand-alone visualization application has been developed by a multi-disciplinary, collaborative team with the sole purpose of creating an interactive exploration environment allowing turbulent flow researchers to experiment and validate hypotheses using visualization. This system has specific optimizations made in data management, caching computations, and visualization allowing for the interactive exploration of datasets on the order of 1TB in size. Using this application, the user (co-author Calo) is able to interactively visualize and analyze all regions of a transitional flow volume, including the laminar, transitional and fully turbulent regions. The underlying goal of the visualizations produced from these transitional flow simulations is to localize turbulent spots in the laminar region of the boundary layer, determine under which conditions they form, and follow their evolution. The initiation of turbulent spots, which ultimately lead to full turbulence, was located via a proposed feature detection condition and verified by experimental results. The conditions under which these turbulent spots form and coalesce are validated and presented.     

Modelling of the lignin peroxidase LIII of Phlebia radiata: use of a sequence template generated from a 3-D structure

A model of the lignin peroxidase LIII of Phlebia radiata wasconstructed on the basis of the structure of cytochrome c peroxidase(CCP). Because of the low percentage of amino acid identitybetween the CCP and the lignin peroxidase LIII of Phlebia radiata,alignment of the sequences was based on the generation of atemplate from a knowledge of the 3-D structure of CCP and consensussequences of lignin peroxidases. This approach gave an alignmentin which all the insertions in the lignin peroxidase were placedat loop regions of CCP, with a 21.1% identity for these twoproteins. The model was constructed using this alignment andthe computer program COMPOSER, which assembles the model asa series of rigid fragments derived from CCP and other proteins.Manual intervention was required for some of the longer loopregions. The -helices forming the structural framework, andespecially the haem environment of CCP, are conserved in theLIII model and the core is close packed without holes. A possiblesite of the substrate oxidation at the haem edge of LIII isdiscussed.