High-aspect-ratio tridimensional electrode arrays for neural applications

Tese de Doutoramento em Engenharia Biomédica.

High performance screen printable lithium-ion battery cathode ink based on C-LiFePO4

Lithium-ion battery cathodes have been fabricated by screen-printing through the development of CLiFePO4 inks. It is shown that shear thinning polymer solutions in N-methyl-2-pyrrolidone (NMP) with Newtonian viscosity above 0.4 Pa s are the best binders for formulating a cathode paste with satisfactory film forming properties. The paste shows an elasticity of the order of 500 Pa and, after shear yielding, shows an apparent viscosity of the order of 3 Pa s for shear rates corresponding to those used during screen-printing. The screen-printed cathode produced with a thickness of 26 mm shows a homogeneous distribution of the active material, conductive additive and polymer binder. The total resistance and diffusion coefficient of the cathode are 450 V and 2.5 10 16cm2 s 1, respectively. The developed cathodes show an initial discharge capacity of 48.2 mAh g 1 at 5C and a discharge value of 39.8 mAh g 1 after 50 cycles. The capacity retention of 83% represents 23% of the theoretical value (charge and/or discharge process in twenty minutes), demonstrating the good performance of the battery. Thus, the developed C-LiFePO4 based inks allow to fabricate screen-printed cathodes suitable for printed lithium-ion batteries

Tapping the wealth of microbial data in high-throughput metabolic model reconstruction

Genome-scale metabolic models are valuable tools in the metabolic engineering process, based on the ability of these models to integrate diverse sources of data to produce global predictions of organism behavior. At the most basic level, these models require only a genome sequence to construct, and once built, they may be used to predict essential genes, culture conditions, pathway utilization, and the modifications required to enhance a desired organism behavior. In this chapter, we address two key challenges associated with the reconstruction of metabolic models: (a) leveraging existing knowledge of microbiology, biochemistry, and available omics data to produce the best possible model; and (b) applying available tools and data to automate the reconstruction process. We consider these challenges as we progress through the model reconstruction process, beginning with genome assembly, and culminating in the integration of constraints to capture the impact of transcriptional regulation. We divide the reconstruction process into ten distinct steps: (1) genome assembly from sequenced reads; (2) automated structural and functional annotation; (3) phylogenetic tree-based curation of genome annotations; (4) assembly and standardization of biochemistry database; (5) genome-scale metabolic reconstruction; (6) generation of core metabolic model; (7) generation of biomass composition reaction; (8) completion of draft metabolic model; (9) curation of metabolic model; and (10) integration of regulatory constraints. Each of these ten steps is documented in detail.

Exploitation of Ashbya gossypii for the production of high-value products from glycerol feedstocks

Dissertação de mestrado em Bioengenharia

Caracterización de moléculas de rizobacterias y de leguminosas con alto impacto productivo y tecnológico en la provincia de Córdoba. Characterization of rhizobacteria and legumes molecules with high production and technological impact in the province of Córdoba.

La provincia de Córdoba cuenta con alto desarrollo agrícola a base de cereales y leguminosas, como por ejemplo el maní. Pero este cultivo con los años ha trasladado su zona de siembra original y se ha extendido hacia otras áreas de mayor riesgo ambiental a raíz de la implantación de la soja. Diversas son las consecuencias de estas dos acciones y que se extienden desde lo agroecológico hasta lo científico-técnico. Este previo estado del arte y las referencias bibliográficas que apuntan a la necesitad de aumentar el valor agregado de los cultivos, nos ha llevado a formular una hipótesis de trabajo y es que las plantas de maní y soja así como las rizobacterias que se asocian con ellas, son productoras de diversas moléculas con potencial uso biológico en la productividad del cultivo y en aplicaciones tecnológicas, biológicas e industriales. Sumado a lo anterior y a las ideas gubernamentales de la necesidad de obtener conocimiento y capitalizarlo como riqueza, y la imperiosa urgencia de responder a demandas regionales, se presenta este proyecto cuyo objetivo general apunta a estudiar la producción de diversas moléculas de rizobacterias y leguminosas con el fin de mejorar la productividad de los cultivos y desarrollar nuevas aplicaciones tecnológicas en la provincia de Córdoba. Para cumplir dentro de los dos años de trabajo solicitados con lo expuesto anteriormente, la investigación será dividida en objetivos específicos y que consisten en investigar la producción de moléculas de raíces de maní y soja, analizar la respuesta microbiana a las rizodeposiciones de ambas leguminosas y evaluar el posible papel biológico y aplicación tecnológica de moléculas de ambos tipos de organismos. Nuestro grupo es de caracter multidisciplinar y ahondará en la diversidad molecular producida por raíces de maní y soja en direfentes días y la respuesta de las rizobacterias que se asocian ellas utilizando técnicas químicas (HPLC, GC, GC-masa) y herramientas microbiológicas y bioquímicas clásicas. Con fines de aplicación tecnológica se determinará la posible acción antioxidante de los extractos vegetales sobre sistemas modelos de ensayo así como la búsqueda de enzimas y hormonas microbianas aplicables en otros campos de la ciencia. De esta forma se pretende atender algunas demandas de diferentes sectores del centro sur de Córdoba y del país pero fundamentalmente posibilitar nuevas aplicaciones de las leguminosas y de las rizobacterias además de permitir la formación académicas de alumnos de grado y posgrado de la UNRC. The province of Cordoba has high agricultural development based on cereals and legumes such as peanuts. But the crop over the years has transferred his original planting area and has spread to other areas of greatest environmental risk following the introduction of soybeans. The previous state and regional art references that point to the necessity of increasing the value-added crops, has led us to formulate a working hypothesis is that the peanut and soybean plants and rhizobacteria associated with they are products of various biological molecules with potential use in crop productivity and biological technology and industrial applications. The general objective is aimed at studying the production of various molecules and legumes rhizobacteria to improve crop productivity and develop new technological applications in the Cordoba province. This form is intended to meet some demands of different sectors of the center south of Cordoba and the country but enabling new applications of legumes and rhizobacteria in addition to allowing the academic training of undergraduates and graduate of the UNRC.

The Irish Pub: past, present – whither the future?

The purpose of this research is to examine the main economic, legislative, and socio- cultural factors that are currently influencing the pub trade in Ireland and their specific impact on a sample of publicans in both Galway city and county. In approaching this task the author engaged in a comprehensive literature review on the origin, history and evolution of the Irish pub; examined the socio-cultural and economic role of the public house in Ireland and developed a profile of the Irish pub by undertaking a number of semi-structured interviews with pub owners from the area. In doing so, the author obtained the views and opinions of the publicans on the current state of their businesses, the extent to which patterns of trade have changed over recent years, the challenges and factors currently influencing their trade, the actions they believed to be necessary to promote the trade and address perceived difficulties and how they viewed the future of the pub business within the framework of the current regulatory regime. In light of this research, the author identified a number of key findings and put forward a series of recommendations designed to promote the future success and development of the pub trade in Ireland. The research established that public houses are currently operating under a very unfavourable regulatory framework that has resulted in the serious decline of the trade over the last decade. This decline appears to have coincided initially with the introduction of the ban on smoking in the workplace and was exacerbated further by the advent of more severe drink-driving laws, especially mandatory breath testing. Other unfavourable conditions include the high levels of excise duty, value added tax and local authority commercial rates. In addition to these regulatory factors, the research established that a major impediment to the pub trade is the unfair competition from supermarkets and other off-licence retail outlets and especially to the phenomenon of the below-cost selling of alcohol. The recession has also been a major contributory factor to the decline in the trade as also has been the trend towards lifestyle changes and home drinking mirroring the practice in some continental European countries.

Training and development in Irish technology companies

The sustained economic growth that has been experienced in the Irish economy in recent years has relied, to a large extent, on the contribution and performance of those industry sectors that possess the ability to provide high-value-added products and services to domestic and international markets. One such contributor has been the Technology sector. However, the performance of this sector relies upon the availability of the necessary capabilities and competencies for Technology companies to remain competitive. The Expert Group on Future Skills Needs have forecasted future skills shortages in this sector. The purpose of this research has been to examine the extent to which Irish Technology companies are taking measures to meet changing skills requirements, through training and development interventions. Survey research methods (in the form of a mail questionnaire, supported by a Web-based questionnaire) have been used to collect information on the expenditure on, and approach to, training and development in these companies, in addition to the methods, techniques and tools/aids that are used to support the delivery of these activities. The contribution of Government intervention has also been examined. The conclusions have been varied. When the activities of the responding companies are considered in isolation, the picture to emerge is primarily positive. Although the expenditure on training and development is slightly lower than that indicated in previous studies, the results vary by company size. Technical employees are clearly the key focus of training provision, while Senior Managers and Directors, Clerical and Administrative staff and Manual workers are a great deal more neglected in training provision. Expenditure on, and use of, computer-based training methods is high, as is the use of most of the specified techniques for facilitating learning. However, when one considers the extent to which external support (in the form of Government interventions and cooperation with other companies and with education and training providers) is integrated into the overall training practices of these companies, significant gaps in practice are identified. The thesis concludes by providing a framework to guide future training and development practices in the Technology sector.

Search for very high energy Gamma radiation from the Starburst Galaxy IC 342

This thesis describes a search for very high energy (VHE) gamma-ray emission from the starburst galaxy IC 342. The analysis was based on data from the 2003 — 2004 observing season recorded using the Whipple 10-metre imaging atmospheric Cherenkov telescope located on Mount Hopkins in southern Arizona. IC 342 may be classed as a non-blazar type galaxy and to date only a few such galaxies (M 87, Cen A, M 82 and NGC 253) have been detected as VHE gamma-ray sources. Analysis of approximately 24 hours of good quality IC 342 data, consisting entirely of ON/OFF observations, was carried out using a number of methods (standard Supercuts, optimised Supercuts, scaled optimised Supercuts and the multivariate kernel analysis technique). No evidence for TeV gamma-ray emission from IC 342 was found. The significance was 0.6 a with a nominal rate of 0.04 ± 0.06 gamma rays per minute. The flux upper limit above 600 GeV (at 99.9 % confidence) was determined to be 5.5 x 10-8 m-2 s-1, corresponding to 8 % of the Crab Nebula flux in the same energy range.

A Grid Supercomputing Enviroment for High Demand Computational Applications

Despite the huge increase in processor and interprocessor network performace, many computational problems remain unsolved due to lack of some critical resources such as floating point sustained performance, memory bandwidth, etc... Examples of these problems are found in areas of climate research, biology, astrophysics, high energy physics (montecarlo simulations) and artificial intelligence, among others. For some of these problems, computing resources of a single supercomputing facility can be 1 or 2 orders of magnitude apart from the resources needed to solve some them. Supercomputer centers have to face an increasing demand on processing performance, with the direct consequence of an increasing number of processors and systems, resulting in a more difficult administration of HPC resources and the need for more physical space, higher electrical power consumption and improved air conditioning, among other problems. Some of the previous problems can´t be easily solved, so grid computing, intended as a technology enabling the addition and consolidation of computing power, can help in solving large scale supercomputing problems. In this document, we describe how 2 supercomputing facilities in Spain joined their resources to solve a problem of this kind. The objectives of this experience were, among others, to demonstrate that such a cooperation can enable the solution of bigger dimension problems and to measure the efficiency that could be achieved. In this document we show some preliminary results of this experience and to what extend these objectives were achieved.

Effect of high pressure processing on the microbiology of skin-vacuum packaged sliced meat products: cooked pork ham, dry cured pork ham and marinated beef loin

High hydrostatic pressure is being increasingly investigated in food processing. It causes microbial inactivation and therefore extends the shelf life and enhances the safety of food products. Yeasts, molds, and vegetative cells of bacteria can be inactivated by pressures in the range of 200 to 700 MPa. Microorganisms are more or less sensitive to pressure depending on several factors such as type, strain and the phase or state of the cells. In general, Gram-positive organisms are usually more resistant than Gram-negative. High pressure processing modifies the permeability of the cell membrane, the ion exchange and causes changes in morphology and biochemical reactions, protein denaturations and inhibition of genetic mechanisms. High pressure has been used successfully to extend the shelf life of high-acid foods such as refrigerated fruit juices, jellies and jams. There is now an increasing interest in the use of this technology to extend the shelf life of low-acid foods such as different types of meat products.

Estudi de la configuració magnètica de l'experiment LTP (LISA Technology Package)

La Teoria de la Relativitat General preveu que quan un objecte massiu és sotmès a una certa acceleració en certes condicions ha d’emetre ones gravitacionals. Es tracta d’un tipus d’on altament energètica però que interacciona amb la matèria de manera molt feble i el seu punt d’emissió és força llunyà. Per la qual cosa la seva detecció és una tasca extraordinàriament complicada. Conseqüentment, la detecció d’aquestes ones es creu molt més factible utilitzant instruments situats a l’espai. Amb aquest objectiu, neis la missió LISA (Laser Interferometer Space Antenna). Es tracta aquesta d’una missió conjunta entre la NASA i l’ESA amb llançament previst per 2020-2025. Per reduir els riscs que comporta una primera utilització de tecnologia no testejada, unit a l’alt cost econòmic de la missió LISA. Aquesta missió contindrà instruments molt avançats: el LTP (LISA Technoplogy Package), desenvolupat per la Unió Europea, que provarà la tecnologia de LISA i el Drag Free flying system, que s’encarregarà de provar una sèrie de propulsors (thrusters) utilitzats per al control d’actitud i posició de satèl•lit amb precisió de nanòmetres. Particularment, el LTP, està composat per dues masses de prova separades per 35 centímetres, i d’un interferòmetre làser que mesura la variació de la distància relativa entre elles. D’aquesta manera, el LTP mesurarà les prestacions dels equips i les possibles interferències que afecten a la mesura. Entre les fonts de soroll es troben, entre d’altres, el vent i pressió de radiació solar, les càrregues electrostàtiques, el gradient tèrmic, les fluctuacions de voltatge o les forces internes. Una de les possibles causes de soroll és aquella que serà l’objecte d’estudi en aquest projecte de tesi doctoral: la presència dintre del LTP de camps magnètics, que exerceixen una força sobre les masses de prova, la seva estimació i el seu control, prenent en compte les caracterírstiques magnètiques de l’experiment i la dinàmica del satèl•lit.

Characterization of the effects of IL-17F on CHO cell line generation

CHO is the most commonly used mammalian host for the generation of cell lines allowing for the production of high quality therapeutic proteins. The generation of such cell lines is a lengthy and resource-intensive process requiring extensive screening in order to isolate candidates with optimal characteristics, such as growth, stability and productivity. For this reason, the biotechnology industry invests much effort in attempts to optimize CHO expression systems in order to streamline and shorten the cell line selection process. Based on preliminary observations of a facilitated selection of CHO-GS cell lines expressing members of the IL-17 cytokine family, this study investigates the use of IL-17F as a novel enhancing factor for CHO cell line generation. Using two different CHO expression systems (exploiting GS and DHFR-based selection), we demonstrated that IL-17F expression caused a significant increase in the occurrence of colonies during the selection process. All colonies selected produced substantial amounts of IL-17F, suggesting that benefits were conferred, during selection, to those cells expressing the cytokine. Furthermore, transgene expression levels were significantly increased when the selection pressure was raised to a level that would not normally be permissive for colony selection (i.e. 100 |o.M MSX for the CHO-GS expression system or 1000 nM MTX for the CHO-DHFR system). Finally, IL-17F expression was also found to enhance the rate of appearance of clones during single cell subcloning in the absence of selection pressure. Overall, these benefits have the potential to allow a substantial reduction in the length of cell line generation while significantly increasing cell line productivity. Nevertheless, we found that the high IL-17F expression levels required to convey enhancing effects was a limitation when attempting to co-express IL-17F and a recombinant soluble protein of therapeutic interest from independent CMV promoters within the same expression vector. In order to understand and overcome this limitation, studies were designed to characterize the IL-17F enhancing effect at the molecular and cellular level. Regular supplementation of recombinant biologically-active IL-17F into the culture medium during cell line selection was not able to reproduce the enhancing effects of endogenous IL-17F expression. In addition, increased IL-17F expression correlated with increased CHO-GS selection transgene expression at the single cell level. This data suggested a possible effect of IL-17F on viral promoter activity or transgene mRNA stability. It also provided direct evidence that the cells expressing the highest amounts of IL-17F obtained the most benefit. Overall data obtained from these study implied that IL-17F may act through an intracellular mechanism, possibly exerted during secretion. We therefore initiated experiments designed to determine the specific compartment(s) within which IL-17F triggers its effect. This work has identified IL-17F as a potentially powerful tool to optimize the CHO cell line generation process. The characterization of this enhancing effect at the molecular level has given us several insights into overcoming the current limitations, thus paving the way for the development of a viable technology that can be exploited within the biotechnology industry. - La CHO est la cellule hôte de mammifere la plus couramment utilisée dans la création de lignée cellulaire produisant des protéines thérapeutiques de haute qualité. La génération de ces lignées cellulaires est un processus long et exigeant l'utilisation de techniques de sélection robustes afin d'isoler des candidats possédants les caractéristiques optimales de croissance, de productivité et de stabilité d'expression. Les industries biopharmaceutiques ont investi beaucoup d'efforts afin d'optimiser les systèmes d'expression CHO dans le but raccourcir la longueur du procédé de sélection de lignées cellulaires et aussi d'en augmenter l'efficacité. A partir d'observations préliminaires obtenues lors de la génération de lignées cellulaires CHO- GS exprimant une cytokine appartenant à la famille des IL-17, nous avons réalisé une étude portant sur l'utilisation de l'IL-17F humaine (IL-17F) comme nouveau facteur d'optimisation pour la génération de lignées cellulaires CHO. Nous avons démontré, en utilisant les deux systèmes de sélection et d'expression CHO couramment utilisés (le premier exploitant la GS et l'autre basée sur la DHFR), que l'expression de l'IL-17F permet une augmentation significative de la fréquence d'apparition de colonies durant le processus de sélection de lignées cellulaires. Les différentes colonies sélectionnées expriment des quantités substantielles d'IL-17F, suggérant un effet bénéfique lors de la sélection qui serait exclusivement conféré aux cellules exprimant la cytokine. En outre, le niveau d'expression du transgene se trouve significativement augmenté lorsque la pression de sélection est portée à un niveau habituellement trop élevé pour permettre la sélection de colonies (soit 100 |JM MSX pour le système d'expression CHO-GS ou 1000 nM MTX pour le système CHO- DHFR). Enfin, l'expression d'IL-17F permet également d'améliorer la vitesse d'apparition de clones pendant une étape de sous-clonage en l'absence de pression de sélection. L'ensemble de ces effets bénéfiques permettent une réduction substantielle de la durée de génération de lignées cellulaires tout en augmentant considérablement la productivité des lignées obtenues. Néanmoins, nous avons constaté que la nécessité d'exprimer des niveaux élevés d'IL-17F afin obtenir l'ensemble de ses effets bénéfiques devient une contrainte lors de l'utilisation d'un vecteur d'expression composé de deux promoteurs CMV indépendants pour la co-expression de la cytokine et d'une protéine soluble présentant un intérêt thérapeutique. Afin de mieux comprendre et de surmonter cette limitation, plusieurs études ont été effectuées dans le but de mieux caractériser l'effet de IL-17F au niveau subcellulaire. L'apport régulier en IL-17F recombinante et biologiquement active dans le milieu de culture lors de la sélection de lignées cellulaires ne permet pas de reproduire les effets bénéfiques observés par l'expression endogène d'IL-17F. En outre, nous avons constaté que, lors de l'utilisation du système CHO- GS, l'augmentation d'expression de 1TL-17F est corrélée à un accroissement de l'expression du marqueur de sélection au niveau cellulaire. Ces résultats suggèrent un possible effet d'IL- 17F sur l'activité des promoteurs viraux et ainsi fournissent une preuve directe que les cellules exprimant de haut niveau d'IL-17F sont celles qui en profitent le plus. L'ensemble de ces observations mettrait en avant que l'effet d'IL-17F se ferait selon un mécanisme intracellulaire. Nous avons donc étudié le(s) compartiment(s) spécifique(s) dans lequel IL-17F pourrait exercer son effet. Ce travail a permis de définir IL-17F comme un puissant outil pour l'optimisation des procédés de génération de lignées cellulaires CHO. La caractérisation de cette amélioration de l'effet au niveau moléculaire nous a donné plusieurs indications sur la manière de dépasser les limitations actuelles, ouvrant ainsi la voie au développement d'une technologie viable qui peut être exploitée pars l'industrie biotechnologique.

Regulatory federalism in network industries

Report for the scientific sojourn at the UC Berkeley, USA, from march until july 2008. This document starts by surveying the literature on economic federalism and relating it to network industries. The insights and some new developments (which focus on the role of interjurisdictional externalities, multiple objectives and investment incentives) are used to analyze regulatory arrangements in telecommunications and energy in the EU and the US. In the long history of vertically integrated monopolies in telecommunications and energy, there was a historical trend to move regulation up in the vertical structure of government, at least form the local level to the state or nation-state level. This move alleviated the pressure on regulators to renege on the commitment not to expropriate sunk investments, although it did not eliminate the practice of taxation by regulation that was the result of multiple interest group action. Although central or federal policy making is more focused and especialized and makes it difficult for more interest groups to organize, it is not clear that under all conditions central powers will not be associated with underinvestment. When technology makes the introduction of competition in some segments possible, the possibilities for organizing the institutional architechture of regulation expand. The central level may focus on structural regulation and the location of behavioral regulation of the remaining monopolists may be resolved in a cooperative way or concentrated at the level where the relevant spillovers are internalized.

Addressing High Level ICT Skills Recruitment Needs

Ireland is a successful major centre for ICT operations with ten of the top ICT companies in the world having substantial operations here. The large talent pool of ICT professionals that exists here is valuable both for foreign-owned and Irish companies. The cluster of internationally renowned firms and Irish companies offer a range of attractive career opportunities for professionals. A range of skills recruitment difficulties have been raised through the work of the Expert Group on Future Skills Needs (EGFSN), specifically the immediate issue of high-level ICT skills within both the ICT sector and from other sectors such as international financial services, banking and business services. Forfs, with the support of IDA Ireland and Enterprise Ireland, engaged in discussions with a selected range of foreign–owned and Irish companies employing approximately 30,000 employees to establish the nature of positions involved, the reasons for recruitment difficulties and to identify measures to help address them. Consultations were also held with key stakeholders including IDA Ireland, Enterprise Ireland, ICT Ireland, Software Ireland, IT@Cork, Engineers Ireland and Dublin Chambers of Commerce. Discussions were held with the heads of the computing departments of all Universities and Institutes of Technology at a meeting chaired by the Higher Education Authority. An in-depth analysis of third-level ICT supply statistics and trends was undertaken to inform the research.