Data management for the ocean sciences - perspectives for the next decade

There is remarkable agreement in expectations today for vastly improved ocean data management a decade from now -- capabilities that will help to bring significant benefits to ocean research and to society. Advancing data management to such a degree, however, will require cultural and policy changes that are slow to effect. The technological foundations upon which data management systems are built are certain to continue advancing rapidly in parallel. These considerations argue for adopting attitudes of pragmatism and realism when planning data management strategies. In this paper we adopt those attitudes as we outline opportunities for progress in ocean data management. We begin with a synopsis of expectations for integrated ocean data management a decade from now. We discuss factors that should be considered by those evaluating candidate “standards”. We highlight challenges and opportunities in a number of technical areas, including “Web 2.0” applications, data modeling, data discovery and metadata, real-time operational data, archival of data, biological data management and satellite data management. We discuss the importance of investments in the development of software toolkits to accelerate progress. We conclude the paper by recommending a few specific, short term targets for implementation, that we believe to be both significant and achievable, and calling for action by community leadership to effect these advancements.

Advanced methods in adaptive control for industrial applications

This volume is based on a seminar concerned with advanced methods in adaptive control for industrial applications which was held in Prague in May 1990 and which brought together experts in the UK and Czechoslovakia in order to suggest solutions to specific current and anticipated problems faced by industry.

Gene-chip technology and its applications

Gene Chips are finding extensive use in animal and plant science. Generally microarrays are of two kind, cDNA or oligonucleotide. cDNA microarrays were developed at Stanford University, whereas oligonucleotide were developed by Affymetrix. The construction of cDNA or oligonucleotide on a glass slide helps to compare the gene expression level of treated and control samples by labeling mRNA with green (Cy3) and red (Cy5) dyes. The hybridized gene chip emit fluorescence whose intensity and colour can be measured. RNA labeling can be done directly or indirectly. Indirect method involves amino allyle modified dUTP instead of pre-labelled nucleotide. Hybridization of gene chip generally occurs in a minimum volume possible and to ensure the hetroduplex formation, a ten fold more DNA is spotted on slide than in the solutions. A confocal or semi confocal laser technologies coupled with CCD camera are used for image acquisition. For standardization, house keeping genes are used or cDNA are spotted in gene chip that are not present in treated or control samples. Moreover, statistical analysis (image analysis) and cluster analysis softwares have been developed by Stanford University. The gene-chip technology has many applications like expression analysis, gene expression signatures (molecular phenotypes) and promoter regulatory element co-expression.

Spatial disaggregation and intensity correction of TRMM-based rainfall time series for hydrological applications in dryland catchments

A novel approach is presented for combining spatial and temporal detail from newly available TRMM-based data sets to derive hourly rainfall intensities at 1-km spatial resolution for hydrological modelling applications. Time series of rainfall intensities derived from 3-hourly 0.25° TRMM 3B42 data are merged with a 1-km gridded rainfall climatology based on TRMM 2B31 data to account for the sub-grid spatial distribution of rainfall intensities within coarse-scale 0.25° grid cells. The method is implemented for two dryland catchments in Tunisia and Senegal, and validated against gauge data. The outcomes of the validation show that the spatially disaggregated and intensity corrected TRMM time series more closely approximate ground-based measurements than non-corrected data. The method introduced here enables the generation of rainfall intensity time series with realistic temporal and spatial detail for dynamic modelling of runoff and infiltration processes that are especially important to water resource management in arid regions.

Applications of micromorphology to understanding activity areas and site formation processes in experimental hut floors

Experimental buildings at Butser Ancient Farm and St. Fagans (UK) and Lejre (Denmark) were sampled to investigate micromorphology of known activity areas, to contribute to our understanding of the internal use of space in excavated buildings and formation processes of house floor deposits. The experimental buildings provided important information relating to activity residues and sediments over the 16 years that the buildings were in use. Specifically, these results contribute to our understanding of the routes and cycles for transportation of materials in occupation contexts, which can be used to inform archaeological studies. It has been possible to identify internal ‘hot spots’ within the buildings for the deposition of activity residues and for the formation of specific deposit types. Analysis also highlighted postdepositional alterations occurring in internal occupation deposits, which has provided a means of identifying roofed and unroofed spaces in the archaeological record.

A cross layer protocol for energy aware and critical data delivered applications using Wireless Sensor Networks

Environment monitoring applications using Wireless Sensor Networks (WSNs) have had a lot of attention in recent years. In much of this research tasks like sensor data processing, environment states and events decision making and emergency message sending are done by a remote server. A proposed cross layer protocol for two different applications where, reliability for delivered data, delay and life time of the network need to be considered, has been simulated and the results are presented in this paper. A WSN designed for the proposed applications needs efficient MAC and routing protocols to provide a guarantee for the reliability of the data delivered from source nodes to the sink. A cross layer based on the design given in [1] has been extended and simulated for the proposed applications, with new features, such as routes discovery algorithms added. Simulation results show that the proposed cross layer based protocol can conserve energy for nodes and provide the required performance such as life time of the network, delay and reliability.

On comparing two sequences of numbers and its applications to clustering analysis

A conceptual problem that appears in different contexts of clustering analysis is that of measuring the degree of compatibility between two sequences of numbers. This problem is usually addressed by means of numerical indexes referred to as sequence correlation indexes. This paper elaborates on why some specific sequence correlation indexes may not be good choices depending on the application scenario in hand. A variant of the Product-Moment correlation coefficient and a weighted formulation for the Goodman-Kruskal and Kendall`s indexes are derived that may be more appropriate for some particular application scenarios. The proposed and existing indexes are analyzed from different perspectives, such as their sensitivity to the ranks and magnitudes of the sequences under evaluation, among other relevant aspects of the problem. The results help suggesting scenarios within the context of clustering analysis that are possibly more appropriate for the application of each index. (C) 2008 Elsevier Inc. All rights reserved.

Random sums of exchangeable variables and actuarial applications

In this paper we study the accumulated claim in some fixed time period, skipping the classical assumption of mutual independence between the variables involved. Two basic models are considered: Model I assumes that any pair of claims are equally correlated which means that the corresponding square-integrable sequence is exchangeable one. Model 2 states that the correlations between the adjacent claims are the same. Recurrence and explicit expressions for the joint probability generating function are derived and the impact of the dependence parameter (correlation coefficient) in both models is examined. The Markov binomial distribution is obtained as a particular case under assumptions of Model 2. (C) 2007 Elsevier B.V. All rights reserved.

Consumed by Faith: The development of Christian Fundamentalism and its applications in contemporary society

My research aims to understand how and why fundamentalists justify violence against people who do not fit their profile of "righteous" or "saved" persons, such as abortion doctors and clinic workers, gays and lesbians, and Jews. The first section of this paper travels through the history of fundamentalism since its origins in the British and American apocalipticism, or belief in the Second Coming of Jesus Christ. However, my history of Protestant Fundamentalism in the United States will focus on the ways in which Fundamentalism developed in response to many changes in American social structure. I interpret Fundamentalism as an anti-modern movement seeking to reassert "traditional" Christian values.

Investigations into the analytical applications and fundamental chemistry of the chemiluminescent reactions of Tris(2,2'-bipyridyl)ruthenium(III) with certain Papaver Somniferum alkaloids and other related compounds

The reaction of tris(2,2’-bipyridyl)ruthenium(III) (Ru(bipy) ₃³⁺) with various analytes to generate chemiluminescence has been well documented. This investigation sought to undertake a chemiluminometic study of the reactions of Ru(bipy) ₃³⁺ with selected Papaver Somniferum alkaloids and specifically synthesised phenethylamines. The investigation, based on a kinetic study, primarily addressed the effect of varying reaction conditions (pH) on Ru(bipy) ₃³⁺ chemiluminescence production. To monitor these reactions, a batch chemiluminometer was specifically designed, fabricated and automated to conduct an extensive study on the selected compounds of interest. The instrumentation incorporated a custom built reaction cell and comprised an ‘on-line’ sample preparation system with which calibration standards could be automatically prepared. The instrumentation provided both time-independent (peak area) and time-dependent (kinetic profile) information. A novel approach to the stabilisation of Ru(bipy) ₃³⁺ as a chemiluminescencent reagent was also investigated and a recirculating system was employed with the batch chemiluminometer to provide a stable supply of Ru(bipy) ₃³⁺. Codeine, thebaine and 6-methoxy-codeine were the Papaver Somniferum alkaloids selected for this study and several N-methylated and N,N-dimethylated phenethylamines and methoxy-substituted phenetheylamines were also synthesised to investigate the affect of pH on the chemiluminescence emission efficiency. The versatility of the batch chemiluminometer facilitated the kinetic study of numerous analytes over a broad pH range. The exemplary performance of the chemiluminometer as an analytical instrument, was demonstrated by the calibration functions, based on peak area data, which exhibited excellent linearity and sensitivity. The estimated detection limits (3s) for the selected alkaloids were in the range 2 x 10^-9 M to 7 x 10^-9 at pH 5.0 and above, which compared favourably to detection limits for the same compounds determined using FIA. Relative standard deviations (n=5) for peak areas ranged between 1% to 5% with a mean of 3.1% for all calibration standards above 2.5 x 10^-8 M. Correlation between concentration and peak area, irrespective of pH and analyte was excellent, with all but two calibration functions having r-squared values greater than 0.990. The analytical figures of merit exemplified the precision and robustness of the reagent delivery and ‘on-line’ sample preparation, as well as the sensitivity of the system. The employment of the chemiluminometer for the measurement of total chemiluminescence emission (peak area) was in itself a feasible analytical technique, which generated highly reproducible and consistent data. Excellent analytical figures of merit, based on peak area, were similarly achieved for the phenethylamines. The effects of analyte structure on chemiluminescence activity was also investigated for the alkaloids and the phenethylamines. Subtle structural variations between the three alkaloids resulted in either a moderately reduced or enhanced total emission that was two or three fold difference only. A significant difference in reaction kinetics was observed between thebaine and codeine/6-methoxy-codeine, which was dependent upon pH. The time-dependent data, namely the observed rate constants for the initial rise in intensity and for the subsequent decay rate, were obtained by fitting a mathematical function (based on the postulated reaction mechanism) to the raw data. The determination of these rate constants for chemiluminescence reactions highlighted the feasibility for utilising such measurements for quantitative analytical applications. The kinetic data were used to discriminate between analyte responses in order to determine the concentrations of individual analytes in a binary mixture. A preliminary, multi-component investigation performed on a binary mixture of codeine and 6-methoxy-codeine (1:1) successfully determined the concentrations of these individual components using such rate constant measurements. Consequently, variations in kinetics resulted in a significant difference between the relative chemiluminescence response based on peak area measurements and the relative response base on peak height measurements obtained using FIA. With regards to the observed reactivity of secondary amines and tertiary amines, chemiluminescence peak area determinations confirmed the vital role of pH on reaction efficiency, which was governed by structural features and kinetics. The tertiary amines investigated generally produced a greater emission under acidic conditions than the corresponding secondary amines. However, the measured chemiluminescence responses were highly dependent upon pH, with similar peak areas obtained for both amine groups under slightly alkaline conditions.

Chemistry, spectroscopy and analytical applications of certain chemiluminescent reactions

Chemiluminescence, the production of light from a chemical reaction, has found widespread use in analytical chemistry. Both tris (2, 2’-bipyridyl) ruthenium (II) and acidic potassium permanganate are chemiluminescence reagents that have been employed for the determination of a diverse range of analytes. This thesis encompasses some fundamental investigations into the chemistry and spectroscopy of these chemiluminescence reactions as well as extending the scope of their analytical applications. Specifically, a simple and robust capillary electrophoresis chemiluminescence detection system for the determination of codeine, O6-methylcodeine and thebaine is described, based upon the reaction of these analytes with chemically generated tris(2,2'-bipyridyl)ruthenium(III) prepared in sulfuric acid (0.05 M). The reagent solution was contained in a glass detection cell, which also held both the capillary and the cathode. The resultant chemiluminescence was monitored directly using a photomultiplier tube mounted flush against the base of the detection cell. The methodology, which incorporated a field amplification sample introduction procedure, realised detection limits (3a baseline noise) of 5 x 10~8 M for both codeine and O6-methylcodeine and 1 x 10~7 M for thebaine. The relative standard deviations of the migration times and the peak areas for the three analytes ranged from 2.2 % up to 2.5 % and 1.9 % up to 4.6 % respectively. Following minor instrumental modifications, morphine, oripavine and pseudomorphine were determined based upon their reaction with acidic potassium permanganate in the presence of sodium polyphosphate. To ensure no migration of the permanganate anion occurred, the anode was placed at the detector end whilst the electroosmotic flow was reversed by the addition of hexadimethrine bromide (0.001% m/v) to the electrolyte. The three analytes were separated counter to the electroosmotic flow via their interaction with a-cyclodextrin. The methodology realised detection limits (3 x S/N) of 2.5 x 10~7 M for both morphine and oripavine and 5 x 10~7 M for pseudomorphine. The relative standard deviations of the migration times and the peak heights for the three analytes ranged from 0.6 % up to 0.8 % and 1.5% up to 2.1 % respectively. Further improvements were made by incorporating a co-axial sheath flow detection cell. The methodology was validated by comparing the results realised using this technique with those obtained by high performance liquid chromatography (HPLC), for the determination of both morphine and oripavine in seven industrial process liquors. A complimentary capillary electrophoresis procedure with UV-absorption detection was also developed and applied to the determination of morphine, codeine, oripavine and thebaine in nine process liquors. The results were compared with those achieved using a standard HPLC method. Although over eighty papers have appeared in the literature on the analytical applications of acidic potassium permanganate chemiluminescence, little effort has been directed towards identifying the origin of the luminescence. It was found that chemiluminescence was generated during the manganese(III), manganese(IV) and manganese(VII) oxidations of sodium borohydride, sodium dithionite, sodium sulfite and hydrazine sulfate in acidic aqueous solution. From the corrected chemiluminescence spectra, the wavelengths of maximum emission were 689 ± 5 nm and 734 ± 5 nm when the reactions were performed in sodium hexametaphosphate and sodium dihydrogenorthophosphate or orthophosphoric acid environments respectively. The corrected phosphorescence spectrum of manganese(II) sulfate in a solution of sodium hexametaphosphate at 77 K, exhibited two peaks with maxima at 688 nm and 730 nm. The chemical and spectroscopic evidence presented strongly supported the postulation that the emission was an example of solution phase chemically induced phosphorescence of manganese(II). Thereby confirming earlier predictions that the chemiluminescence from acidic potassium permanganate reactions originated from an excited manganese(II) species. Additionally, these findings have had direct analytical application in that manganese(IV) was evaluated as a new reagent for chemiluminescence detection. The oxidations of twenty five organic and inorganic species, with solublised manganese(IV), were found to elicit analytically useful chemiluminescence with detection limits (3 x S/N) for Mn(II), Fe(II), morphine and codeine of 5 x 10-8 M, 2.5 x 10-7 M, 7.5 x 10-8 M and 5 x 10-8M, respectively. The corrected emission spectra from four different analytes gave wavelengths of maximum emission in the range from 733 nm up to 740 nm indicating that these chemiluminescence reactions also shared a common emitting species, excited manganese(II). Whilst several analytical problems were addressed in this thesis and answers to certain questions regarding the fundamentals of acidic potassium permanganate chemiluminescence were proposed, there are several areas that would benefit from further research. These are outlined in the final chapter of this thesis.

Applications and fundamental understanding of selected analytically important chemiluminescence reactions

This thesis encompasses a series of investigations into the fundamental chemistry and spectroscopy of chemiluminescence (chemical reactions that produce light). This new knowledge enabled the development of innovative analytical methodologies for rapid chemical measurements in forensic science, industrial process monitoring and clinical diagnostics.

Investigation of abalone mitochondrial DNA and new applications

The work developed and applied new mitochondrial DNA markers to abalone aquaculture and wild fisheries. The number of markers and their success in the areas applied were all firsts in the abalone industry. The work will contribute to the future sustainability of this resource in culture and in the wild.