Remote sensing of spatio-temporal relationships between the partitioned absorption coefficients of phytoplankton cells and mineral particles and euphotic zone depths in a partially mixed shelf sea

AbstractAbsorption coefficients for mineral particles and phytoplankton cells in the 488nm waveband, aMSS(488) and aCHL(488), and euphotic zone depths, z1%PAR, were determined for the Irish Sea and St. George's Channel from 8years of MODIS remote sensing reflectance observations. The results are presented as composite maps of the entire region for the months of January, April, July and October and as time series averaged over 2week intervals for three selected locations representing different mixing regimes. Annual cycles in aMSS(488) were observed in most areas, with maximum values occurring in winter when increased vertical mixing brought fine sediments to the surface. Euphotic depths were strongly influenced by aMSS(488) cycles, but sharp reductions were superimposed wherever phytoplankton blooms occurred. A key hydrographic feature of this region is the formation of a front in St. George's Channel between mixed and seasonally stratified water bodies. On the mixed side of the front, single peaks in aCHL(488) were observed in summer when the euphotic zone was at its deepest. On the stratified side, double peaks in aCHL(488) occurred in spring and autumn while low summer values of aCHL(488) coincided with high values of z1%PAR. The remote sensing evidence indicates, therefore, that phytoplankton growth (as reflected by net accumulation at the surface) in summer was limited by light availability in mixed waters, and nutrient availability in the stratified region. We conclude that observations of spatio-temporal patterns in phytoplankton and mineral particle absorption coefficients and euphotic depths derived from ocean colour sensors can provide insights into the processes determining the depth of penetration of solar radiation, and also the factors limiting near-surface primary production, in optically complex and spatially heterogeneous shelf seas

Derivation of the specific optical properties of suspended mineral particles and their contribution to the attenuation of solar irradiance in offshore waters by ocean color remote sensing

Two independently derived algorithms which had previously been validated against in situ data were applied to 8 years of MODIS observations of the Irish Sea to obtain (i) concentrations of lithogenic mineral particles (MSSl) in surface waters and (ii) the specific backscattering and absorption coefficients for these particles in the 488 nm waveband (the values obtained were a*MSSl488=0.031 m2 g-1 and bb*MSSl488=0.010 m2 g-1). This information was used to calculate the mean attenuation coefficient for downward irradiance K-d(488) in the surface mixed layer, and the fraction of this coefficient that was attributable to suspended mineral particles. Mineral particles at relatively low concentrations (<5 g m-3) were the major determinant of K-d(488) values throughout the region in winter, and in the central Irish Sea this influence persisted for much of the spring/autumn primary production period. In the north and south, however, marked short-term increases in K-d(488) due to phytoplankton blooms occurred during periods when MSSl values were relatively low. Seasonally averaged maps of the fractional contribution of MSSl to K-d(488) show strong links to vertical mixing, with sharp contrasts developing in spring at the boundaries between mixed and stratified waters. We conclude that the ocean color processing sequence presented here can reveal spatial and seasonal patterns in the dynamics of lithogenic mineral particles which have potentially valuable applications in ecosystem status assessment, environmental impact monitoring, and the tuning and validation of numerical models of shelf sea ecosystems

Clinical software development for the Web: lessons learned from the BOADICEA project.

BACKGROUND: In the past 20 years, society has witnessed the following landmark scientific advances: (i) the sequencing of the human genome, (ii) the distribution of software by the open source movement, and (iii) the invention of the World Wide Web. Together, these advances have provided a new impetus for clinical software development: developers now translate the products of human genomic research into clinical software tools; they use open-source programs to build them; and they use the Web to deliver them. Whilst this open-source component-based approach has undoubtedly made clinical software development easier, clinical software projects are still hampered by problems that traditionally accompany the software process. This study describes the development of the BOADICEA Web Application, a computer program used by clinical geneticists to assess risks to patients with a family history of breast and ovarian cancer. The key challenge of the BOADICEA Web Application project was to deliver a program that was safe, secure and easy for healthcare professionals to use. We focus on the software process, problems faced, and lessons learned. Our key objectives are: (i) to highlight key clinical software development issues; (ii) to demonstrate how software engineering tools and techniques can facilitate clinical software development for the benefit of individuals who lack software engineering expertise; and (iii) to provide a clinical software development case report that can be used as a basis for discussion at the start of future projects. RESULTS: We developed the BOADICEA Web Application using an evolutionary software process. Our approach to Web implementation was conservative and we used conventional software engineering tools and techniques. The principal software development activities were: requirements, design, implementation, testing, documentation and maintenance. The BOADICEA Web Application has now been widely adopted by clinical geneticists and researchers. BOADICEA Web Application version 1 was released for general use in November 2007. By May 2010, we had > 1200 registered users based in the UK, USA, Canada, South America, Europe, Africa, Middle East, SE Asia, Australia and New Zealand. CONCLUSIONS: We found that an evolutionary software process was effective when we developed the BOADICEA Web Application. The key clinical software development issues identified during the BOADICEA Web Application project were: software reliability, Web security, clinical data protection and user feedback.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Studying Human Relatedness through a Shared Gaming Experience

The importance of relatedness in collocated multiplayer video games should not be underestimated. Interpersonal relationships which develop from social interactions that occur during gameplay contribute to player motivation and meaningful and memorable experiences for the players. In this study we examined how interpersonal touch within a gameplay experience impacted player motivation and inter-player impressions. Dyads played one of two iPad-based games in three different conditions, one of which required physical contact between the players. Results indicated those in the touch-based conditions scored higher on several measures of intrinsic motivation and impressions of their teammate

Brewster-angle measurements of sea-surface reflectance using a high resolution spectroradiometer

This paper describes the design, construction and testing of a ship-borne spectroradiometer based on an imaging spectrograph and cooled CCD array with a wavelength range of 350-800 nm and 4 nm spectral sampling. The instrument had a minimum spectral acquisition time of 0.1 s, but in practice data were collected over periods of 10 s to allow averaging of wave effects. It was mounted on a ship's superstructure so that it viewed the sea surface from a height of several metres at the Brewster angle (53 degrees) through a linear polarizing filter. Comparison of sea-leaving spectra acquired with the polarizer oriented horizontally and vertically enabled estimation of the spectral composition of sky light reflected directly from the sea surface. A semi-empirical correction procedure was devised for retrieving water-leaving radiance spectra from these measurements while minimizing the influence of reflected sky light. Sea trials indicated that reflectance spectra obtained by this method were consistent with the results of radiance transfer modelling of case 2 waters with similar concentrations of chlorophyll and coloured dissolved organic matter. Surface reflectance signatures measured at three locations containing blooms of different phytoplankton species were easily discriminated and the instrument was sufficiently sensitive to detect solar-stimulated fluorescence from surface chlorophyll concentrations down to 1 mg m−3

System and method for delivering a graphical user interface of remote applications over a thin bandwidth connection

A method and system are disclosed for delivering interactive links for presenting applications and second information at a client computer from remote sources in a network-configured computer processing system. In one embodiment, the method includes retrieving over a first communication connection, in response to a request of a client computer, informational content having computer program code embedded therein, and executing the embedded computer program code for establishing a second communication connection to an application server. The method further includes retrieving over the second communication connection first information including presentational information for presenting the application and the second information. The method also includes presenting the application and the second information based upon the presentational information, and storing on the client computer an interactive link for selectively re-establishing the second communication connection to the application server for retrieving the first information and presenting the application and the second information on an as-needed basis. Preferably, the storing of the interactive link includes downloading a graphical representation of the interactive link and storing a file containing information representing an operating environment of the client computer and a network address of the application server.Published versio

Culturable diversity of bacterial endophytes associated with medicinal plants of the Western Ghats, India

Bacterial endophytes are found in the internal tissues of plants and have intimate associations with their host. However, little is known about the diversity of medicinal plant endophytes (ME) or their capability to produce specialised metabolites that may contribute to therapeutic properties. We isolated 75 bacterial ME from 24 plant species of the Western Ghats, India. Molecular identification by 16S rRNA gene sequencing grouped MEs into 13 bacterial genera, with members of Gammaproteobacteria and Firmicutes being the most abundant. To improve taxonomic identification, 26 selected MEs were genome sequenced and average nucleotide identity (ANI) used to identify them to the species-level. This identified multiple species in the most common genus as Bacillus. Similarly, identity of the Enterobacterales was also distinguished within Enterobacter and Serratia by ANI and core-gene analysis. AntiSMASH identified non-ribosomal peptide synthase, lantipeptide and bacteriocin biosynthetic gene clusters (BGC) as the most common BGCs found in the ME genomes. A total of five of the ME isolates belonging to Bacillus, Serratia and Enterobacter showed antimicrobial activity against the plant pathogen Pectobacterium carotovorum. Using molecular and genomic approaches we have characterised a unique collection of endophytic bacteria from medicinal plants. Their genomes encode multiple specialised metabolite gene clusters and the collection can now be screened for novel bioactive and medicinal metabolites

The power of co-ordinate transformations in dynamical interpretations of Galactic structure

$Gaia$ DR2 has provided an unprecedented wealth of information about the positions and motions of stars in our Galaxy, and has highlighted the degree of disequilibria in the disc. As we collect data over a wider area of the disc it becomes increasingly appealing to start analysing stellar actions and angles, which specifically label orbit space, instead of their current phase space location. Conceptually, while $\bar{x}$ and $\bar{v}$ tell us about the potential and local interactions, grouping in action puts together stars that have similar frequencies and hence similar responses to dynamical effects occurring over several orbits. Grouping in actions and angles refines this further to isolate stars which are travelling together through space and hence have shared histories. Mixing these coordinate systems can confuse the interpretation. For example, it has been suggested that by moving stars to their guiding radius, the Milky Way spiral structure is visible as ridge-like overdensities in the $Gaia$ data \citep{Khoperskov+19b}. However, in this work, we show that these features are in fact the known kinematic moving groups, both in the $L_z-\phi$ and the $v_{\mathrm{R}}-v_{\phi}$ planes. Using simulations we show how this distinction will become even more important as we move to a global view of the Milky Way. As an example, we show that the radial velocity wave seen in the Galactic disc in $Gaia$ and APOGEE should become stronger in the action-angle frame, and that it can be reproduced by transient spiral structure.Comment: 12 pages, 10 Figure