Models for persistence in lazy functional programming systems

Research into providing support for long term data in lazy functional programming systems is presented in this thesis. The motivation for this work has been to reap the benefits of integrating lazy functional programming languages and persistence. The benefits are: the programmer need not write code to support long term data since this is provided as part of the programming system; persistent data can be used in a type safe way since the programming language type system applies to data with the whole range of persistence; the benefits of lazy evaluation are extended to the full lifetime of a data value. Whilst data is reachable, any evaluation performed on the data persists. A data value changes monotonically from an unevaluated state towards a completely evaluated state over time. Interactive data intensive applications such as functional databases can be developed. These benefits are realised by the development of models for persistence in lazy functional programming systems. Two models are proposed which make persistence available to the functional programmer. The first, persistent modules, allows values named in modules to be stored in persistent storage for later reuse. The second model, stream persistence allows dynamic, interactive access to persistent storage. These models are supported by a system architecture which incorporates a persistent abstract machine, PCASE, integrated with a persistent object store. The resulting persistent lazy functional programming system, Staple, is used in prototyping and functional database modelling experiments

Laser machined macro and micro structures on glass for enhanced light trapping in solar cells

In order to increase the efficiency of solar cell modules it is necessary to make the optimum use of light incident upon them. Much research has been done on improving light absorption through front surface texturisation and light trapping schemes. Laser light is commonly used in industry for various applications including marking and texturisation. By controlling laser parameters, it is possible to tailor macro and micro structures in most materials. The CO2 laser used in this investigation emits radiation at 10.6 μm with the ability to pulse in the micro-second range. The laser was used to ablate grooved textures in the fused quartz material, used in this study as the light trapping medium, following which an analysis of the effects of the laser parameters on the texture geometry and surface morphology was performed through a combination of cross sectioning and scanning electron microscopy. Transmission through the textured glass was improved for most samples after acid etching. The light trapping effects of the best performing textures were analysed by investigating the effects on a silicon solar cell’s performance at varying angles of incidence. Results indicated a significant increase in light trapping when light was incident at acute angles. For an angle of incidence of 10◦ a relative increase in efficiency of up to 51 % was observed

Famine Early Warning Systems Network (FEWS NET) Land Data Assimilation System (LDAS) and Other Assimilated Hydrological Data at NASA GES DISC

The NASA Goddard Earth Sciences Data and Information Services Center (GES DISC) provides science support for several data sets relevant to agriculture and food security, including the Famine Early Warning Systems Network (FEWS NET) Land Data Assimilation System (LDAS), or FLDAS data set. The GES DISC is one of twelve NASA Earth Observing System (EOS) data centers that process, archive, document, and distribute data from Earth science missions and related projects. The GES DISC hosts a wide range of remote sensing and model data, and provides reliable and robust data access and other services to users worldwide. Beyond data archive and access, the GES DISC offers many services to visualize and analyze the data. This presentation provides a summary of the hydrological data available at the GES DISC, along with an overview of related data services. Specifically, the FLDAS data set has been adapted to work with domains, data streams, and monitoring and forecast requirements associated with food security assessment in data-sparse, developing country settings. The FLDAS global monthly data have a 0.1 x 0.1 degree spatial resolution covering the period from January 1982 to present. Global FLDAS monthly anomaly and monthly climatology data are also available at the GES DISC to evaluate how current conditions compare to averages over the FLDAS 35-year period. Several case studies using the FLDAS soil moisture, evapotranspiration, rainfall, runoff, and surface temperature data will be presented

Biosynthesis of UDP-N-acetyl-L-fucosamine, a precursor to the biosynthesis of lipopolysaccharide in Pseudomonas aeruginosa serotype O11.

Abstract UDP-N-acetyl-l-fucosamine is a precursor to l-fucosamine in the lipopolysaccharide of Pseudomonas aeruginosa serotype O11 and the capsule of Staphylococcus aureus type 5. We have demonstrated previously the involvement of three enzymes, WbjB, WbjC, and WbjD, in the biosynthesis of UDP-2-acetamido-2,6-dideoxy-l-galactose or UDP-N-acetyl-l-fucosamine (UDP-l-FucNAc). An intermediate compound from the coupled-reaction of WbjB-WbjC with the initial substrate UDP-2-acetamido-2-deoxy-α-d-glucose or UDP-N-acetyl-d-glucosamine (UDP-GlcNAc) was purified, and the structure was determined by NMR spectroscopy to be UDP-2-acetamido-2,6-dideoxy-l-talose (UDP-l-PneNAc). WbjD could then convert this intermediate into a new product with the same mass, consistent with a C-2 epimerization reaction. Those results led us to propose a pathway for the biosynthesis of UDP-l-FucNAc; however, the exact enzymatic activity of each of these proteins has not been defined. Here, we describe a fast protein liquid chromatography (FPLC)-based anion-exchange procedure, which allowed the separation and purification of the products of C-2 epimerization due to WbjD. Also, the application of a cryogenically cooled probe in NMR spectrometry offers the greatest sensitivity for determining the structures of minute quantities of materials, allowing the identification of the final product of the pathway. Our results showed that WbjB is bifunctional, catalyzing firstly C-4, C-6 dehydration and secondly C-5 epimerization in the reaction with the substrate UDP-d-GlcNAc, producing two intermediates. WbjC is also bifunctional, catalyzing C-3 epimerization of the second intermediate followed by reduction at C-4. The FPLC-based procedure provided good resolution of the final product of WbjD reaction from its epimer/substrate UDP-l-PneNAc, and the use of the cryogenically cooled probe in NMR revealed unequivocally that the final product is UDP-l-FucNAc

Rice Molecular Breeding Laboratories in the Genomics Era: Current Status and Future Considerations

Using DNA markers in plant breeding with marker-assisted selection (MAS) could greatly improve the precision and efficiency of selection, leading to the accelerated development of new crop varieties. The numerous examples of MAS in rice have prompted many breeding institutes to establish molecular breeding labs. The last decade has produced an enormous amount of genomics research in rice, including the identification of thousands of QTLs for agronomically important traits, the generation of large amounts of gene expression data, and cloning and characterization of new genes, including the detection of single nucleotide polymorphisms. The pinnacle of genomics research has been the completion and annotation of genome sequences for indica and japonica rice. This information—coupled with the development of new genotyping methodologies and platforms, and the development of bioinformatics databases and software tools—provides even more exciting opportunities for rice molecular breeding in the 21st century. However, the great challenge for molecular breeders is to apply genomics data in actual breeding programs. Here, we review the current status of MAS in rice, current genomics projects and promising new genotyping methodologies, and evaluate the probable impact of genomics research. We also identify critical research areas to “bridge the application gap” between QTL identification and applied breeding that need to be addressed to realize the full potential of MAS, and propose ideas and guidelines for establishing rice molecular breeding labs in the postgenome sequence era to integrate molecular breeding within the context of overall rice breeding and research programs

Diversification of Colonization Factors in a Multidrug-Resistant Escherichia coli Lineage Evolving under Negative Frequency-Dependent Selection

Escherichia coli is a major cause of bloodstream and urinary tract infections globally. The wide dissemination of multidrug-resistant (MDR) strains of extraintestinal pathogenic E. coli (ExPEC) poses a rapidly increasing public health burden due to narrowed treatment options and increased risk of failure to clear an infection. Here, we present a detailed population genomic analysis of the ExPEC ST131 clone, in which we seek explanations for its success as an emerging pathogenic strain beyond the acquisition of antimicrobial resistance (AMR) genes. We show evidence for evolution toward separate ecological niches for the main clades of ST131 and differential evolution of anaerobic metabolism, key colonization, and virulence factors. We further demonstrate that negative frequency-dependent selection acting across accessory loci is a major mechanism that has shaped the population evolution of this pathogen.IMPORTANCE Infections with multidrug-resistant (MDR) strains of Escherichia coli are a significant global public health concern. To combat these pathogens, we need a deeper understanding of how they evolved from their background populations. By understanding the processes that underpin their emergence, we can design new strategies to limit evolution of new clones and combat existing clones. By combining population genomics with modelling approaches, we show that dominant MDR clones of E. coli are under the influence of negative frequency-dependent selection, preventing them from rising to fixation in a population. Furthermore, we show that this selection acts on genes involved in anaerobic metabolism, suggesting that this key trait, and the ability to colonize human intestinal tracts, is a key step in the evolution of MDR clones of E. coli.Peer reviewe

Silicon enhances the accumulation of diterpenoid phytoalexins in rice: A potential mechanism for blast resistance

Although several reports underscore the importance of silicon (Si) in controlling Magnaporthe grisea on rice, no study has associated this beneficial effect with specific mechanisms of host defense responses against this fungal attack. In this study, however, we provide evidence that higher levels of momilactone phytoalexins were found in leaf extracts from plants inoculated with M. grisea and amended with silicon (Si+) than in leaf extracts from inoculated plants not amended with silicon (Si-) or noninoculated Si+ and Si- plants. On this basis, the more efficient stimulation of the terpenoid pathway in Si+ plants and, consequently, the increase in the levels of momilactones appears to be a factor contributing to enhanced rice resistance to blast. This may explain the lower level of blast severity observed on leaves of Si+ plants at 96 h after inoculation with M. grisea. The results of this study strongly suggest that Si plays an active role in the resistance of rice to blast rather than the formation of a physical barrier to penetration by M. grisea

Facile preparation of starch-based electroconductive films with ionic liquid

Here, we discovered that starch could be straightforwardly processed into optically-transparent electroconductive films, by compression molding at a relatively mild temperature (55 °C or 65 °C), much lower than those commonly used in biopolymer melt processing (typically over 150 °C). Such significantly-reduced processing temperature was achieved with the use of an ionic liquid plasticizer, 1-ethyl-3-methylimidazolium acetate ([C2mim][OAc]). A higher [C2mim][OAc] content, lower processing temperature (55 °C), and/or higher relative humidity (RH) (75%) during the sample post-processing conditioning, suppressed the crystallinity of the processed material. The original A-type crystalline structure of starch was eliminated, although small amounts of B-type and V-type crystals were formed subsequently. The starch crystallinity could be linked to the mechanical properties of the films. Moreover, the processing destroyed the original lamellar structure of starch, and the amorphous starch processed with [C2mim][OAc]/water could aggregate on the nanoscale. The films displayed excellent electrical conductivity (> 10−3 S/cm), which was higher with a lower processing temperature (55 °C) and a higher conditioning RH (75%). The incorporation of [C2mim][OAc] reduced the thermal decomposition temperature of starch by 30 °K, while the formulation and processing conditions did not affect the film thermal stability

Composition of dissolved organic matter within a lacustrine environment

Freshwater dissolved organic matter (DOM) is a complex mixture of chemical components that are central to many environmental processes, including carbon and nitrogen cycling. However, questions remain as to its chemical characteristics, sources and transformation mechanisms. Here, we employ 1- and 2-D nuclear magnetic resonance (NMR) spectroscopy to investigate the structural components of lacustrine DOM from Ireland, and how it varies within a lake system, as well as to assess potential sources. Major components found, such as carboxyl-rich alicyclic molecules (CRAM) are consistent with those recently identified in marine and freshwater DOM. Lignin-type markers and protein/peptides were identified and vary spatially. Phenylalanine was detected in lake areas influenced by agriculture, whereas it is not detectable where zebra mussels are prominent. The presence of peptidoglycan, lipoproteins, large polymeric carbo- hydrates and proteinaceous material supports the substantial contribution of material derived from microorganisms. Evidence is provided that peptidoglycan and silicate species may in part originate from soil microbes

The transformation of earth-system observations into information of socio-economic value in GEOSS

The Group on Earth Observations System of Systems, GEOSS, is a co-ordinated initiative by many nations to address the needs for earth-system information expressed by the 2002 World Summit on Sustainable Development. We discuss the role of earth-system modelling and data assimilation in transforming earth-system observations into the predictive and status-assessment products required by GEOSS, across many areas of socio-economic interest. First we review recent gains in the predictive skill of operational global earth-system models, on time-scales of days to several seasons. We then discuss recent work to develop from the global predictions a diverse set of end-user applications which can meet GEOSS requirements for information of socio-economic benefit; examples include forecasts of coastal storm surges, floods in large river basins, seasonal crop yield forecasts and seasonal lead-time alerts for malaria epidemics. We note ongoing efforts to extend operational earth-system modelling and assimilation capabilities to atmospheric composition, in support of improved services for air-quality forecasts and for treaty assessment. We next sketch likely GEOSS observational requirements in the coming decades. In concluding, we reflect on the cost of earth observations relative to the modest cost of transforming the observations into information of socio-economic value