Theoretical investigations prompted by experiments with baroclinic fluids

Imperial Users onl

Provenance, propagation and quality of biological annotation

PhD ThesisBiological databases have become an integral part of the life sciences, being used to store, organise and share ever-increasing quantities and types of data. Biological databases are typically centred around raw data, with individual entries being assigned to a single piece of biological data, such as a DNA sequence. Although essential, a reader can obtain little information from the raw data alone. Therefore, many databases aim to supplement their entries with annotation, allowing the current knowledge about the underlying data to be conveyed to a reader. Although annotations come in many di erent forms, most databases provide some form of free text annotation. Given that annotations can form the foundations of future work, it is important that a user is able to evaluate the quality and correctness of an annotation. However, this is rarely straightforward. The amount of annotation, and the way in which it is curated, varies between databases. For example, the production of an annotation in some databases is entirely automated, without any manual intervention. Further, sections of annotations may be reused, being propagated between entries and, potentially, external databases. This provenance and curation information is not always apparent to a user. The work described within this thesis explores issues relating to biological annotation quality. While the most valuable annotation is often contained within free text, its lack of structure makes it hard to assess. Initially, this work describes a generic approach that allows textual annotations to be quantitatively measured. This approach is based upon the application of Zipf's Law to words within textual annotation, resulting in a single value, . The relationship between the value and Zipf's principle of least e ort provides an indication as to the annotations quality, whilst also allowing annotations to be quantitatively compared. Secondly, the thesis focuses on determining annotation provenance and tracking any subsequent propagation. This is achieved through the development of a visualisation - i - framework, which exploits the reuse of sentences within annotations. Utilising this framework a number of propagation patterns were identi ed, which on analysis appear to indicate low quality and erroneous annotation. Together, these approaches increase our understanding in the textual characteristics of biological annotation, and suggests that this understanding can be used to increase the overall quality of these resources

Linking seasonal forecasts into RiskView to enhance food security contingency planning

RiskView is a tool developed by the World Food Programme (WFP) to translate weather data (real-time and historical) and other spatial information (e.g., crops, drought risk, population, etc.) into food security needs and response costs. It serves as a swift way of estimating costs in advance of food insecurity outlooks for financial planning, and for facilitating better resource allocations to disasters before on-the-ground needs assessments are produced

Low C18 to C20 fatty acid elongase activity and limited conversion of stearidonic acid, 18:4(n-3), to eicosapentaenoic acid, 20:5(n-3), in a cell line from the turbot, Scophthalmus maximus

The TF cell line, derived from a top predatory, carnivorous marine teleost, the turbot (Scophthalmus maximus), is known to have a limited conversion of C18 to C20 polyunsaturated fatty acids (PUFA). To illuminate the underlying processes, we studied the conversions of stearidonic acid, 18:4(n-3), and its elongation product, 20:4(n-3), in TF cells and also in a cell line, AS, derived from Atlantic salmon (Salmo salar), by adding unlabelled (25 uM), U-14C (1 uM) or deuterated (d5; 25 uM) fatty acids. Stearidonic acid, 18:4(n-3), was metabolised to 20:5(n-3) in both cells lines, but more so in AS than in TF cells. Delta-5 desaturation was more active in TF cells than in AS cells, whereas C18 to C20 elongation was much reduced in TF as compared to AS cells. Only small amounts of docosahexaenoic acid (22:6(n-3)) were produced by both cell lines, although there was significant production of 22:5(n-3) in both cultures, especially when 20:4(n-3) was supplemented. We conclude that limited elongation of C18 to C20 fatty acids rather than limited fatty acyl Delta-5 desaturation accounts for the limited rate of conversion of 18:3(n-3) to 20:5(n-3) in the turbot cell line, as compared to the Atlantic salmon cell line. The results can account for the known differences in conversions of C18 to C20 PUFA by the turbot and the Atlantic salmon in vivo

Timeseries partitioning of ecosystem respiration components in seasonal, non-tropical forests; comparing literature derived coefficients with evaluation at two contrasting UK forest sites

Funding The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This work was supported by UK Research and Innovation and the Biotechnology and Biological Research Council through the Strategic Priorities Fund for Greenhouse Gas Removal. NetZeroPlus: Sustainable Treescapes Demonstrator and Decision Tools (Netzeroplus.ac.uk), Grant number BB/V011588/1. The Alice Holt 2010 soil flux data were collected as part of a Natural Environment Research Council (NERC grants: F14/G6/105 & NE/C513550/1) funded project Centre for Terrestrial Carbon Dynamics. Acknowledgments The authors would like to thank Prof. Jo Smith at Aberdeen University for comments and suggestions on an early draft, and special thanks to Edward Eaton for assisting with running the Alice Holt site and contributing to the soil flux measurements. We are further grateful to the Forestry Commission, UK, for funding both the Alice Holt and Harwood long-term research sites.Peer reviewe

Dust aerosol, clouds, and the atmospheric optical depth record over 5 Mars years of the Mars Exploration Rover mission

Dust aerosol plays a fundamental role in the behavior and evolution of the Martian atmosphere. The first five Mars years of Mars Exploration Rover data provide an unprecedented record of the dust load at two sites. This record is useful for characterization of the atmosphere at the sites and as ground truth for orbital observations. Atmospheric extinction optical depths have been derived from solar images after calibration and correction for time-varying dust that has accumulated on the camera windows. The record includes local, regional, and globally extensive dust storms. Comparison with contemporaneous thermal infrared data suggests significant variation in the size of the dust aerosols, with a 1 {\mu}m effective radius during northern summer and a 2 {\mu}m effective radius at the onset of a dust lifting event. The solar longitude (LS) 20-136{\deg} period is also characterized by the presence of cirriform clouds at the Opportunity site, especially near LS=50 and 115{\deg}. In addition to water ice clouds, a water ice haze may also be present, and carbon dioxide clouds may be present early in the season. Variations in dust opacity are important to the energy balance of each site, and work with seasonal variations in insolation to control dust devil frequency at the Spirit site.Comment: 60 pages, 12 figures, to be published in Icaru

Expanding the Capability of Satellite Operations using a Global Federated Ground Station Network

Small-scale spaceflight programs such as those found at universities and start-up companies may operate satellites from a single ground station. This station’s location may not be optimal for radio communications, and a single station limits the contact time available to conduct operations. The idea of a global federated ground station network (FGN) has been theorized in the past, and with today’s wide-spread internet connectivity it is now possible for such a network to exist. One example of an FGN that is functioning today is an open-source project called SatNOGS. The Michigan eXploration Laboratory (MXL) at the University of Michigan has applied the benefits of this network to enhance operations of their Tandem Beacon Experiment (TBEx) CubeSat mission by gathering 2.2x the beacons gathered by their home station alone. 93% of those additional beacons were collected by six SatNOGS stations. Augmenting MXL’s home station with these six stations increases access time to the TBEx satellites by a factor of 5 to15. This increased temporal coverage also enabled MXL operators to identify their spacecraft after deployment and correct an error causing the TBEx radios to function intermittently, saving the mission in its earliest days

The LOFAR Magnetism Key Science Project

Measuring radio waves at low frequencies offers a new window to study cosmic magnetism, and LOFAR is the ideal radio telescope to open this window widely. The LOFAR Magnetism Key Science Project (MKSP) draws together expertise from multiple fields of magnetism science and intends to use LOFAR to tackle fundamental questions on cosmic magnetism by exploiting a variety of observational techniques. Surveys will provide diffuse emission from the Milky Way and from nearby galaxies, tracking the propagation of long-lived cosmic-ray electrons through magnetic field structures, to search for radio halos around spiral and dwarf galaxies and for magnetic fields in intergalactic space. Targeted deep-field observations of selected nearby galaxies and suspected intergalactic filaments allow sensitive mapping of weak magnetic fields through Rotation Measure (RM) grids. High-resolution observations of protostellar jets and giant radio galaxies reveal structures on small physical scales and at high redshifts, whilst pulsar RMs map large-scale magnetic structures of the Galactic disk and halo in revolutionary detail. The MKSP is responsible for the development of polarization calibration and processing, thus widening the scientific power of LOFAR.Comment: Proceedings of "Magnetic Fields in the Universe: From Laboratory and Stars to Primordial Structures", 2011 Aug. 21-27 in Zakopane/Poland, eds. M. Soida et a

The structural role of elastic fibres in the cornea investigated using a mouse model for Marfan syndrome

Purpose: The presence of fibrillin-rich elastic fibers in the cornea has been overlooked in recent years. The aim of the current study was to elucidate their functional role using a mouse model for Marfan syndrome, defective in fibrillin-1, the major structural component of the microfibril bundles that constitute most of the elastic fibers. Methods: Mouse corneas were obtained from animals with a heterozygous fibrillin-1 mutation (Fbn1+/−) and compared to wild type controls. Corneal thickness and radius of curvature were calculated using optical coherence tomography microscopy. Elastic microfibril bundles were quantified and visualized in three-dimensions using serial block face scanning electron microscopy. Transmission electron microscopy was used to analyze stromal ultrastructure and proteoglycan distribution. Center-to-center average interfibrillar spacing was determined using x-ray scattering. Results: Fbn1+/− corneas were significantly thinner than wild types and displayed a higher radius of curvature. In the Fbn1+/− corneas, elastic microfibril bundles were significantly reduced in density and disorganized compared to wild-type controls, in addition to containing a higher average center-to-center collagen interfibrillar spacing in the center of the cornea. No other differences were detected in stromal ultrastructure or proteoglycan distribution between the two groups. Proteoglycan side chains appeared to colocalize with the microfibril bundles. Conclusions: Elastic fibers have an important, multifunctional role in the cornea as highlighted by the differences observed between Fbn1+/− and wild type animals. We contend that the presence of normal quantities of structurally organized elastic fibers are required to maintain the correct geometry of the cornea, which is disrupted in Marfan syndrome

Development and Application of a Simple Plaque Assay for the Human Malaria Parasite Plasmodium falciparum.

Malaria is caused by an obligate intracellular protozoan parasite that replicates within and destroys erythrocytes. Asexual blood stages of the causative agent of the most virulent form of human malaria, Plasmodium falciparum, can be cultivated indefinitely in vitro in human erythrocytes, facilitating experimental analysis of parasite cell biology, biochemistry and genetics. However, efforts to improve understanding of the basic biology of this important pathogen and to develop urgently required new antimalarial drugs and vaccines, suffer from a paucity of basic research tools. This includes a simple means of quantifying the effects of drugs, antibodies and gene modifications on parasite fitness and replication rates. Here we describe the development and validation of an extremely simple, robust plaque assay that can be used to visualise parasite replication and resulting host erythrocyte destruction at the level of clonal parasite populations. We demonstrate applications of the plaque assay by using it for the phenotypic characterisation of two P. falciparum conditional mutants displaying reduced fitness in vitro