The Synthesis of Arbitrary Stable Dynamics in Non-linear Neural Networks II: Feedback and Universality

We wish to construct a realization theory of stable neural networks and use this theory to model the variety of stable dynamics apparent in natural data. Such a theory should have numerous applications to constructing specific artificial neural networks with desired dynamical behavior. The networks used in this theory should have well understood dynamics yet be as diverse as possible to capture natural diversity. In this article, I describe a parameterized family of higher order, gradient-like neural networks which have known arbitrary equilibria with unstable manifolds of known specified dimension. Moreover, any system with hyperbolic dynamics is conjugate to one of these systems in a neighborhood of the equilibrium points. Prior work on how to synthesize attractors using dynamical systems theory, optimization, or direct parametric. fits to known stable systems, is either non-constructive, lacks generality, or has unspecified attracting equilibria. More specifically, We construct a parameterized family of gradient-like neural networks with a simple feedback rule which will generate equilibrium points with a set of unstable manifolds of specified dimension. Strict Lyapunov functions and nested periodic orbits are obtained for these systems and used as a method of synthesis to generate a large family of systems with the same local dynamics. This work is applied to show how one can interpolate finite sets of data, on nested periodic orbits.

Market-oriented new product development of functional beverages

Strategic reviews of the Irish Food and Beverage Industry have consistently emphasised the need for food and beverage firms to improve their innovation and marketing capabilities, in order to maintain competitiveness in both domestic and overseas markets. In particular, the functional food and beverages market has been singled out as an extremely important emerging market, which Irish firms could benefit from through an increased technological and market orientation. Although health and wellness have been the most significant drivers of new product development (NPD) in recent years, failure rates for new functional foods and beverages have been reportedly high. In that context, researchers in the US, UK, Denmark and Ireland have reported a marked divergence between NPD practices within food and beverage firms and normative advice for successful product development. The high reported failure rates for new functional foods and beverages suggest a failure to manage customer knowledge effectively, as well as a lack of knowledge management between functional disciplines involved in the NPD process. This research explored the concept of managing customer knowledge at the early stages of the NPD process, and applied it to the development of a range of functional beverages, through the use of advanced concept optimisation research techniques, which provided for a more market-oriented approach to new food product development. A sequential exploratory research design strategy using mixed research methods was chosen for this study. First, the qualitative element of this research investigated customers’ choice motives for orange juice and soft drinks, and explored their attitudes and perceptions towards a range of new functional beverage concepts through a combination of 15 in-depth interviews and 3 focus groups. Second, the quantitative element of this research consisted of 3 conjoint-based questionnaires administered to 400 different customers in each study in order to model their purchase preferences for chilled nutrient-enriched and probiotic orange juices, and stimulant soft drinks. The in-depth interviews identified the key product design attributes that influenced customers’ choice motives for orange juice. The focus group discussions revealed that groups of customers were negative towards the addition of certain functional ingredients to natural foods and beverages. K-means cluster analysis was used to quantitatively identify segments of customers with similar preferences for chilled nutrient-enriched and probiotic orange juices, and stimulant soft drinks. Overall, advanced concept optimisation research methods facilitate the integration of the customer at the early stages of the NPD process, which promotes a multi-disciplinary approach to new food product design. This research illustrated how advanced concept optimisation research methods could contribute towards effective and efficient knowledge management in the new food product development process.

Biodiscovery of natural products from microbes associated with Irish coastal sponges

Marine sponges have been an abundant source of new metabolites in recent years. The symbiotic association between the bacteria and the sponge has enabled scientists to access the bacterial diversity present within the bacterial/sponge ecosystem. This study has focussed on accessing the bacterial diversity in two Irish coastal marine sponges, namely Amphilectus fucorum and Eurypon major. A novel species from the genus Aquimarina has been isolated from the sponge Amphilectus fucorum. The study has also resulted in the identification of an α–Proteobacteria, Pseudovibrio sp. as a potential producer of antibiotics. Thus a targeted based approach to specifically cultivate Pseudovibrio sp. may prove useful for the development of new metabolites from this particular genus. Bacterial isolates from the marine sponge Haliclona simulans were screened for anti–fungal activity and one isolate namely Streptomyces sp. SM8 displayed activity against all five fungal strains tested. The strain was also tested for anti–bacterial activity and it showed activity against both against B. subtilis and P. aeruginosa. Hence a combinatorial approach involving both biochemical and genomic approaches were employed in an attempt to identify the bioactive compounds with these activities which were being produced by this strain. Culture broths from Streptomyces sp. SM8 were extracted and purified by various techniques such as reverse–phase HPLC, MPLC and ash chromatography. Anti–bacterial activity was observed in a fraction which contained a hydroxylated saturated fatty acid and also another compound with a m/z 227 but further structural elucidation of these compounds proved unsuccessful. The anti–fungal fractions from SM8 were shown to contain antimycin–like compounds, with some of these compounds having different retention times from that of an antimycin standard. A high–throughput assay was developed to screen for novel calcineurin inhibitors using yeast as a model system and three putative bacterial extracts were found to be positive using this screen. One of these extracts from SM8 was subsequently analysed using NMR and the calcineurin inhibition activity was con rmed to belong to a butenolide type compound. A H. simulans metagenomic library was also screened using the novel calcineurin inhibitor high–throughput assay system and eight clones displaying putative calcineurin inhibitory activity were detected. The clone which displayed the best inhibitory activity was subsequently sequenced and following the use of other genetic based approaches it became clear that the inhibition was being caused by a hypothetical protein with similarity to a hypothetical Na+/Ca2+ exchanger protein. The Streptomyces sp. SM8 genome was sequenced from a fragment library using Roche 454 pyrosequencing technology to identify potential secondary metabolism clusters. The draft genome was annotated by IMG/ER using the Prodigal pipeline. The Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession AMPN00000000. The genome contains genes which appear to encode for several polyketide synthases (PKS), non–ribosomal peptide synthetases (NRPS), terpene and siderophore biosynthesis and ribosomal peptides. Transcriptional analyses led to the identification of three hybrid clusters of which one is predicted to be involved in the synthesis of antimycin, while the functions of the others are as yet unknown. Two NRPS clusters were also identified, of which one may be involved in gramicidin biosynthesis and the function of the other is unknown. A Streptomyces sp. SM8 NRPS antC gene knockout was constructed and extracts from the strain were shown to possess a mild anti–fungal activity when compared to the SM8 wild–type. Subsequent LCMS analysis of antC mutant extracts confirmed the absence of the antimycin in the extract proving that the observed anti–fungal activity may involve metabolite(s) other than antimycin. Anti–bacterial activity in the antC gene knockout strain against P. aeruginosa was reduced when compared to the SM8 wild–type indicating that antimycin may be contributing to the observed anti–bacterial activity in addition to the metabolite(s) already identified during the chemical analyses. This is the first report of antimycins exhibiting anti–bacterial activity against P. aeruginosa. One of the hybrid clusters potentially involved in secondary metabolism in SM8 that displayed high and consistent levels of gene–expression in RNA studies was analysed in an attempt to identify the metabolite being produced by the pathway. A number of unusual features were observed following bioinformatics analysis of the gene sequence of the cluster, including a formylation domain within the NRPS cluster which may add a formyl group to the growing chain. Another unusual feature is the lack of AT domains on two of the PKS modules. Other unusual features observed in this cluster is the lack of a KR domain in module 3 of the cluster and an aminotransferase domain in module 4 for which no clear role has been hypothesised.

Synthesis of 4-substituted-3(2H)-furanones with novel luminescence properties

The objective of this project was to prepare a range of 4-substituted 3-(2H)-furanones, and to investigate the relationship between their molecular structures and photoluminescence properties. The effects of substituents and conjugated linker unit were also investigated. After generation of the key 3(2H)-furanone heterocycle, extension of the conjugated framework at the C-4 position was achieved through Pd(0)-catalysed coupling reactions. Chapter one of the thesis comprises a review of the relavent literature and is split into three sections. These include information about the prevalence of 3-(2H)-furanones as natural products and synthetic routes to 3-(2H)-furanones in general. The synthetic routes are divided according to the synthetic precursor employed. The final section of chapter one outlines the fundamental principles and application of photoluminescence to organic compounds in general. Chapter two contains the results of the research achieved in the course of this work and a discussion of the findings. Two routes were successfully employed to generate 4-unsubstituted 3-(2H)-furanone moieties: (i) base induced cyclisation of hydroxyenones and (ii) isoxazole chemistry. A number of methods which proved ineffective in the production of furanones with the desired substitution pattern are also detailed. The majority of this study was focused on the introduction of substituents at the C-4 position of the 3-(2H)-furanone ring. This was achieved through the use of Sonogashira and Suzuki cross coupling protocols for Pd(0) catalysed C-C bond formation. The further functionalisation of some compounds was performed using transfer hydrogenation and “click chemistry” methodologies. Finally, the photophysical properties of 3-(2H)-furanones prepared in this project are discussed and the effect of substitution patterns in a complementary “push push” and “push pull” manner have also been investigated. All the experimental data and details of the synthetic methods employed, for the compounds prepared during the course of this research is contained in chapter three together with the spectroscopic and analytical properties of the compounds prepared.

Non-product related environmental process and production methods (NPR-PPMs): a view from international trade law and international environmental governance

The primary aim of this thesis is to analyse legal and governance issues in the use of Environmental NPR-PPMs, particularly those aiming to promote sustainable practices or to protect natural resources. NPR-PPMs have traditionally been thought of as being incompatible with the rules of the World Trade Organization (WTO). However, the issue remains untouched by WTO adjudicatory bodies. One can suggest that WTO adjudicatory bodies may want to leave this issue to the Members, but the analysis of the case law also seems to indicate that the question of legality of NPR-PPMs has not been brought ‘as such’ in dispute settlement. This thesis advances the argument that despite the fact that the legal status of NPR-PPMs remains unsettled, during the last decades adjudicatory bodies have been scrutinising environmental measures based on NPR-PPMs just as another expression of the regulatory autonomy of the Members. Though NPR-PPMs are regulatory choices associated with a wide range of environmental concerns, trade disputes giving rise to questions related to the legality of process-based measures have been mainly associated with the protection of marine wildlife (i.e., fishing techniques threatening or affecting animal species). This thesis argues that environmental objectives articulated as NPR-PPMs can indeed qualify as legitimate objectives both under the GATT and the TBT Agreement. However, an important challenge for the their compatibility with WTO law relate to aspects associated with arbitrary or unjustifiable discrimination. In the assessment of discrimination procedural issues play an important role. This thesis also elucidates other important dimensions to the issue from the perspective of global governance. One of the arguments advanced in this thesis is that a comprehensive analysis of environmental NPR-PPMs should consider not only their role in what is regarded as trade barriers (governmental and market-driven), but also their significance in global objectives such as the transition towards a green economy and sustainable patterns of consumption and production.

The potential of natural, photosynthetic pigments to improve the efficiency of dye-sensitized solar cells

Gemstone Team Grenergy

Natural hybridization between genera that diverged from each other approximately 60 million years ago.

A fern from the French Pyrenees-×Cystocarpium roskamianum-is a recently formed intergeneric hybrid between parental lineages that diverged from each other approximately 60 million years ago (mya; 95% highest posterior density: 40.2-76.2 mya). This is an extraordinarily deep hybridization event, roughly akin to an elephant hybridizing with a manatee or a human with a lemur. In the context of other reported deep hybrids, this finding suggests that populations of ferns, and other plants with abiotically mediated fertilization, may evolve reproductive incompatibilities more slowly, perhaps because they lack many of the premating isolation mechanisms that characterize most other groups of organisms. This conclusion implies that major features of Earth's biodiversity-such as the relatively small number of species of ferns compared to those of angiosperms-may be, in part, an indirect by-product of this slower "speciation clock" rather than a direct consequence of adaptive innovations by the more diverse lineages.

La aplicación estratégica por escenarios en el medio natural. El caso del Nature Outlook 2050 del PBL.

La prospectiva es parte de la planificación estratégica. Es una herramienta habitual en la gestión y dirección de empresas. Algunos países europeos la incluyen dentro de sus trabajos de diseño de las políticas ambientales. La generación de escenarios es una técnica cualitativa de prospectiva apta para los entornos con alta variabilidad y complejidad. El artículo explica el modo de aplicar esta técnica poniendo en paralelo los pasos dados en el proyecto Nature Outlook 2050 que ha desarrollado la agencia de evaluación y prospectiva ambiental de los Países Bajos (PBL).

Solid-phase synthesis of terminal oligonucleotide-phosphoramidate conjugates

A novel phosphoramidite, N,N-diisopropylamino-2-cyanoethyl-9-anthracenemethyl phosphoramidite 1, was prepared and coupled with the terminal 5'-hydroxyl of support-bound T10 and the putative phosphite triester intermediate was subsequently reacted with iodine in the presence of either water or a series of primary and secondary amines. The reactivity of 1 compared to a previously reported benzyl phosphoramidite 2 was also investigated: oxidation of the product of coupling 2 with CPG-T10-5'OH under aqueous conditions resulted in greater than 30% of the benzyl moiety being retained. In contrast, essentially complete loss of the 9-anthracenemethyl group was observed using 1 under the same conditions. Oligonucleotides modified with a terminal phosphate monoester, lipophilic, fluorescent or cationic groups were thus prepared.

Maleimide spacers as versatile linkers in the synthesis of bioconjugates of anthracyclines

This review covers the structural design and versatile use of maleimide spacers in the preparation of bioconjugates of the anthracyclines doxorubicin and daunorubicin. It underpins the research conducted in our group on the preparation of conjugates of daunorubicin and transferrin.

Evidence that the major degradation product of glucose-dependent insulinotropic polypeptide, GIP(3-42), is a GIP receptor antagonist in vivo

The incretin hormone glucose-dependent insulinotropic polypeptide (GIP) is rapidly degraded in the circulation by dipeptidyl peptidase IV forming the N-terminally truncated peptide GIP(3-42). The present study examined the biological activity of this abundant circulating fragment peptide to establish its possible role in GIP action. Human GIP and GIP(3-42) were synthesised by Fmoc solid-phase peptide synthesis, purified by HPLC and characterised by electrospray ionisation-mass spectrometry. In GIP receptor-transfected Chinese hamster lung fibroblasts, GIP(3-42) dose dependently inhibited GIP-stimulated (10(-7) M) cAMP production (up to 75.4 +/-5.4%; P

A DFT study of the chain growth probability in Fischer-Tropsch synthesis

The chain growth probability (alpha value) is one of the most significant parameters in Fischer-Tropsch (FT) synthesis. To gain insight into the chain growth probability, we systematically studied the hydrogenation and C-C coupling reactions with different chain lengths on the stepped Co(0001) surface using density functional theory calculations. Our findings elucidate the relationship between the barriers of these elementary reactions and the chain length. Moreover, we derived a general expression of the chain growth probability and investigated the behavior of the alpha value observed experimentally. The high methane yield results from the lower chain growth rate for C-1 + C-1 coupling compared with the other coupling reactions. After C-1, the deviation of product distribution in FT synthesis from the Anderson-Schulz-Flory distribution is due to the chain length-dependent paraffin/olefin ratio. (C) 2008 Elsevier Inc. All rights reserved.

Synthesis of 3-(4-tert-butylphenyl)-2-propen-1-one, a precursor to Lilial (R), via an aldol condensation in an ionic liquid

An efficient synthesis of a precursor to Lilial(R), based on an aldol condensation in an ionic liquid, is described, utilising piperidine as the base catalyst. The yields obtained with this methodology are significantly increased in comparison with those reported in organic solvents to date. In the ionic liquid, the self-aldol condensation of propanal is suppressed and leads to an increased selectivity with respect to the cross-aldol condensation product without the need to use an excess of 4-tert-butylbenzaldehyde to obtain high selectivities.

Selective synthesis of chlorophosphoramidites using ionic liquids

A range of chlorophosphoramidites have been prepared in ionic liquids and compared with material synthesised in molecular solvents. Through the use of ionic liquids as reaction media the moisture sensitivity and impurity issues hampering existing traditional synthetic routes have been eased. Not only can stock chemicals be used without purification, but the reactions may be conducted at room temperature and at high concentrations. Furthermore, reaction times are reduced and rapid addition of reagents is possible whilst retaining tight control over product selectivity. Beyond their role as reaction media, ionic liquids also present a unique storage medium for these highly moisture sensitive chlorophosphoramidites.

Synthesis of a tetraoxy-bis-nortaxadiene, en route to taxol, using a cascade radical cyclisation sequence

Concise syntheses of the substituted enynediones 28a, 33b and 36 starting from the cyclohexenealdehyde 18, corresponding to ring A in the taxanes, and the vinylstannane 24, are described. Treatment of 36 with Bu3SnH–AIBN did not lead to the oxy-substituted taxadiene 37 expected from a tandem radical macrocyclisation–radical transannulation sequence; instead, a mixture of unidentified products resulted. When the PMB ether 33b corresponding to the alcohol 36 was treated with Bu3SnH–AIBN under similar conditions, p-anisaldehyde was isolated, as a major by-product, but no evidence for the formation of a taxadiene could be observed. In contrast, the iododienynedione 41, i.e., deoxy 36, underwent a tandem radical macrocyclisation–transannulation sequence, when treated with Bu3SnH–AIBN, leading to the tetraoxy-bis-nortaxadiene 42 in 44% yield. Attempts to synthesise the alcohol 28b from the silyl ether 28a en route to the iodide 28c instead gave the substituted tetrahydrofuran 29 via an intramolecular oxy-Michael reaction.