Extracting predictive models from marked-p free-text documents at the Royal Botanic Gardens, Kew, London

In this paper we explore the combination of text-mining, un-supervised and supervised learning to extract predictive models from a corpus of digitised historical floras. These documents deal with the nomenclature, geographical distribution, ecology and comparative morphology of the species of a region. Here we exploit the fact that portions of text in the floras are marked up as different types of trait and habitat. We infer models from these different texts that can predict different habitat-types based upon the traits of plant species. We also integrate plant taxonomy data in order to assist in the validation of our models. We have shown that by clustering text describing the habitat of different floras we can identify a number of important and distinct habitats that are associated with particular families of species along with statistical significance scores. We have also shown that by using these discovered habitat-types as labels for supervised learning we can predict them based upon a subset of traits, identified using wrapper feature selection

Weather and the epidemiology of the African Armyworm (Spodoptera exempta) (NRI Bulletin 58)

Armyworm reports and weather records for eastern Africa were analysed for armyworm seasons from 1972-88. Relationships between the frequency and distribution of outbreaks and weather (especially wind and rainfall) were summarized for each season separately and compared between seasons. The work reported in this bulletin will enable armyworm forecasters in eastern Africa to compare present and past seasons, predict how seasons might develop, and improve forecasts. The results are being used to assess the economic viability of strategic control

On the Hyperbolicity of Lorenz Renormalization

We consider infinitely renormalizable Lorenz maps with real critical exponent $\alpha>1$ and combinatorial type which is monotone and satisfies a long return condition. For these combinatorial types we prove the existence of periodic points of the renormalization operator, and that each map in the limit set of renormalization has an associated unstable manifold. An unstable manifold defines a family of Lorenz maps and we prove that each infinitely renormalizable combinatorial type (satisfying the above conditions) has a unique representative within such a family. We also prove that each infinitely renormalizable map has no wandering intervals and that the closure of the forward orbits of its critical values is a Cantor attractor of measure zero.Comment: 63 pages; 10 figure

Natural variation in ovule morphology is influenced by multiple tissues and impacts downstream grain development in barley (Hordeum vulgare L.).

The ovule plays a critical role in cereal yield as it is the site of fertilization and the progenitor of the grain. The ovule primordium is generally comprised of three domains, the funiculus, chalaza, and nucellus, which give rise to distinct tissues including the integuments, nucellar projection, and embryo sac. The size and arrangement of these domains varies significantly between model eudicots, such as Arabidopsis thaliana, and agriculturally important monocotyledonous cereal species, such as Hordeum vulgare (barley). However, the amount of variation in ovule development among genotypes of a single species, and its functional significance, remains unclear. To address this, wholemount clearing was used to examine the details of ovule development in barley. Nine sporophytic and gametophytic features were examined at ovule maturity in a panel of 150 European two-row spring barley genotypes, and compared with grain traits from the preceding and same generation. Correlations were identified between ovule traits and features of grain they produced, which in general highlighted a negative correlation between nucellus area, ovule area, and grain weight. We speculate that the amount of ovule tissue, particularly the size of the nucellus, may affect the timing of maternal resource allocation to the fertilized embryo sac, thereby influencing subsequent grain development.Laura G. Wilkinson, Xiujuan Yang, Rachel A. Burton, Tobias Würschum and Matthew R. Tucke

Earthshine observation of vegetation and implication for life detection on other planets - A review of 2001 - 2006 works

The detection of exolife is one of the goals of very ambitious future space missions that aim to take direct images of Earth-like planets. While associations of simple molecules present in the planet's atmosphere ($O_2$, $O_3$, $CO_2$ etc.) have been identified as possible global biomarkers, we review here the detectability of a signature of life from the planet's surface, i.e. the green vegetation. The vegetation reflectance has indeed a specific spectrum, with a sharp edge around 700 nm, known as the "Vegetation Red Edge" (VRE). Moreover vegetation covers a large surface of emerged lands, from tropical evergreen forest to shrub tundra. Thus considering it as a potential global biomarker is relevant. Earthshine allows to observe the Earth as a distant planet, i.e. without spatial resolution. Since 2001, Earthshine observations have been used by several authors to test and quantify the detectability of the VRE in the Earth spectrum. The egetation spectral signature is detected as a small 'positive shift' of a few percents above the continuum, starting at 700 nm. This signature appears in most spectra, and its strength is correlated with the Earth's phase (visible land versus visible ocean). The observations show that detecting the VRE on Earth requires a photometric relative accuracy of 1% or better. Detecting something equivalent on an Earth-like planet will therefore remain challenging, moreover considering the possibility of mineral artifacts and the question of 'red edge' universality in the Universe.Comment: Invited talk in "Strategies for Life Detection" (ISSI Bern, 24-28 April 2006) to appear in a hardcopy volume of the ISSI Space Science Series, Eds, J. Bada et al., and also in an issue of Space Science Reviews. 13 pages, 8 figures, 1 tabl

Dose-dependent AGO1-mediated inhibition of the miRNA165/166 pathway modulates stem cell maintenance in Arabidopsis shoot apical meristem

Pluripotent stem cells localized in proliferating growth centers, the meristems, are the origin of life-long organ formation and growth in higher plants. In the shoot apical meristem of Arabidopsis thaliana, the closely related ARGONAUTE proteins AGO1 and ZLL/AGO10 bind miR165/166 species to regulate mRNAs of HD-ZIP III transcription factors that are essential to maintaining stem cells. Several genetic studies showed that AGO1 and ZLL/AGO10 act redundantly to maintain stem cells. By contrast, the reported biochemical data suggested antagonistic functions: AGO1 utilizes miR165/166 to slice HD-ZIP III mRNAs, whereas ZLL/AGO10 promotes degradation of miR165/166 and thus stabilizes HD-ZIP III mRNAs. How these different functions are balanced in stem cell regulation has remained enigmatic. Here, we show that autorepression of AGO1 through miR168-mediated slicing of its own RNA is required to maintain the ability of AGO1 to suppress HD-ZIP III mRNAs. Increased AGO1 expression, either in the miR168a-2 mutant or by transgenic expression, inhibits this ability despite the presence of high levels of miR165/166, effectively uncoupling HD-ZIP III and miR165/166 expression. AGO1 activity can be restored, however, by increasing the levels of chaperones SQN and HSP90, which promote assembly of RNA-induced silencing complex (RISC). This suggests that cellular abundance of SQN and HSP chaperones limits AGO1-mediated RNA interference in shoot meristem stem cell regulation. Localized misexpression of AGO1 indicates that the cells surrounding the shoot meristem primordium play a crucial role in stem cell development. Taken together, our study provides a framework that reconciles biochemical and genetic data, showing that restriction of AGO1 levels by miR168-mediated autorepression is key to RISC homeostasis and the function of AGO1 in stem cell regulation.Fei Du, Wen Gong, Sonia Bosca, Matthew Tucker, Herve, Vaucheret, and Thomas Lau

An investigation of using grey scale image analysis for predicting the amount of deposited electrospun nanofibres

When electrospinning, the amount of electrospun fibres deposited is difficult to determine due to the extremely small size and light weight of the fibres. Several methods have been used to predict the amount of deposited fibres including weighing, imaging and direct measurement. Although these methods work to a certain extent, they all have drawbacks that make them unsuitable for commercial scale process control. The methods are generally time consuming, destructive and only examine a small area of web. In this study, an image analysis method is used to predict the amount of electrospun fibres deposited over a significant area. When images of electrospun fibres are converted into grey scale images, it is suggested that the amount of fibres deposited can be predicted by measuring the grey scale intensity. A conventional weighing method was used to validate the image analysis results. The weighing method was found wanting when the deposition time was short (p>0.05). This was because the measured fibre masses were insignificant compared to the weight variation of the collector substrates. Statistical analyses showed that there were a strong correlation between grey scale intensity and deposition time especially at short deposition times. The results suggest that image analysis method could be used to predict the amount of deposited electrospun nanofibres. Further test on different polymers and different coloured substrates showed that the method was still capable to distinguish the samples. The developed method has the potential to be applied as an in-line non-destructive quality control method for electrospun fibre manufacture

HvSL1 and HvMADS16 promote stamen identity to restrict multiple ovary formation in barley

OnlinePublCorrect floral development is the result of a sophisticated balance of molecular cues. Floral mutants provide insight into the main genetic determinants that integrate these cues, as well as providing opportunities to assess functional variation across species. In this study, we characterize the barley (Hordeum vulgare) multiovary mutants mov2.g and mov1, and propose causative gene sequences: a C2H2 zinc-finger gene HvSL1 and a B-class gene HvMADS16, respectively. In the absence of HvSL1, florets lack stamens but exhibit functional supernumerary carpels, resulting in multiple grains per floret. Deletion of HvMADS16 in mov1 causes homeotic conversion of lodicules and stamens into bract-like organs and carpels that contain non-functional ovules. Based on developmental, genetic, and molecular data, we propose a model by which stamen specification in barley is defined by HvSL1 acting upstream of HvMADS16. The present work identifies strong conservation of stamen formation pathways with other cereals, but also reveals intriguing species-specific differences. The findings lay the foundation for a better understanding of floral architecture in Triticeae, a key target for crop improvement.Caterina Selva, Xiujuan Yang, Neil J. Shirley, Ryan Whitford, Ute Baumann and Matthew R. Tucke

Ovule cell wall composition is a maternal determinant of grain size in barley

OnlinePublIn cereal species, seed and grain size is influenced by growth of the ovule integuments (seed coat), the spikelet hull (lemma and palea) and the filial endosperm. It has remained unclear whether a highly conserved ovule tissue, the nucellus, has any impact on grain size. Immunolabelling revealed that the barley nucellus comprises two distinct cell types that differ in terms of cell wall homogalacturonan (HG) accumulation. Transcriptional profiling of the nucellus identified two pectin methylesterase genes, OVULE PECTIN MODIFIER 1 (OPM1) and OPM2, which are expressed in the ovule but absent from the seed. Ovules from an opm1 opm2 mutant, and plants expressing an ovule-specific pectin methylesterase inhibitor (PMEI), exhibit reduced HG accumulation. This results in changes to ovule cell size and shape, and ovules that are longer than wild-type controls. At grain maturity, this is manifested as significantly longer grain. These findings indicate that cell wall composition during ovule development acts to limit ovule and seed growth. The investigation of ovule PME and PMEI activity reveals an unexpected role of maternal tissues in controlling grain growth prior to fertilisation, one that has been lacking from models exploring improvements in grain size.Xiujuan Yang, Laura G. Wilkinson, Matthew K. Aubert, Kelly Houston, Neil J. Shirley, and Matthew R. Tucke

Design and Development of Domestic Cyclone Dust Collector System Using TRIZ And CCD Method

In conventional vacuum cleaners, filter media or filter bags are used to physically separate dust and debris from flowing air streams. However, in such systems, the vacuum cleaner's efficiency diminishes over time as more debris is accumulated on the filter surface. In this study, a two-stage cyclone dust collector system was proposed, which can be attached to existing vacuum cleaners. The system was designed and developed using the integrated Theory of Inventive Problem Solving (TRIZ) and Classical Cyclone Design (CCD) method. The TRIZ method was implemented during the idea generation stage, where specific design solution strategies were reviewed. Theoretical analysis of the selected design was carried out using Classical Cyclone Design (CCD) method. Finally, a full-scale working prototype of the cyclone dust collector was fabricated for evaluation. Based on results, the cyclone dust collector system provides more than 99% fractional efficiency and 96% overall collection efficiency for particles with an average diameter of over 50 μm. The pressure drops and airflow inside the cyclone dust collector were also analysed. The results suggest that the proposed cyclone dust collector system would provide better filtration efficiency and less maintenance compared to the conventional system