A systems biology framework for pathway level culture media engineering: pplication to Pichia pastoris cultures

Dissertação para obtenção do Grau de Doutor em Engenharia Química e Bioquímica

Evolving team compositions by agent swapping

Optimizing collective behavior in multiagent systems requires algorithms to find not only appropriate individual behaviors but also a suitable composition of agents within a team. Over the last two decades, evolutionary methods have emerged as a promising approach for the design of agents and their compositions into teams. The choice of a crossover operator that facilitates the evolution of optimal team composition is recognized to be crucial, but so far, it has never been thoroughly quantified. Here, we highlight the limitations of two different crossover operators that exchange entire agents between teams: restricted agent swapping (RAS) that exchanges only corresponding agents between teams and free agent swapping (FAS) that allows an arbitrary exchange of agents. Our results show that RAS suffers from premature convergence, whereas FAS entails insufficient convergence. Consequently, in both cases, the exploration and exploitation aspects of the evolutionary algorithm are not well balanced resulting in the evolution of suboptimal team compositions. To overcome this problem, we propose combining the two methods. Our approach first applies FAS to explore the search space and then RAS to exploit it. This mixed approach is a much more efficient strategy for the evolution of team compositions compared to either strategy on its own. Our results suggest that such a mixed agent-swapping algorithm should always be preferred whenever the optimal composition of individuals in a multiagent system is unknown.

Sterolin valmistus selluprosessin yhteydessä

Työssä tutkittiin UPM-Kymmene Oyj Kaukaan kemiallisella tehtaalla käytössä olevia steroliprosesseja. Steroleita erotetaan sulfaattiselluloosan keitossa syntyvasta suovasta uutetusta neutraaliainejakeesta. Neutraaliaine sisältää β-sitosterolia, α-sitosterolia ja kampesterolia yhteensä noin 20 p-%. Primal-laadun valmistus perustuu neste-nesteuuttoon sekä kiteytykseen ja Ultra-laadun kaksivaiheiseen suorakiteytykseen. Työn kirjallisessa osassa perehdytään sterolien kemiaan sekä neste-nesteuuttoon ja kiteytykseen erotus- ja puhdistusmenetelminä. Laboratoriokokeissa tutkittiin kolmen eri alkoholin ja kahden eri hiilivetyliuottimen soveltuvuutta Primal-sitosterolin uuttoon ja kiteytykseen. Lisaksi tutkittiin liuotinseoksen vesipitoisuuden vaikutusta. Tavoitteena oli löytää uuttoliuottimien koostumus, jolla uuton sterolisaanto ja sterolikiteiden puhtaus olisivat mahdollisimman korkeat. Havaittiin, että uuton sterolisaanto voitiin maksimoida pitämällä uuttoalkoholin vesipitoisuus niin alhaisena, että faasit juuri ja juuri erottuvat toisistaan. Laboratoriokokeissa saatujen tulosten perusteella tehtiin tehdasmittakaavan koeajo Primal-sitosterolin valmistuslaitteistolla UPM-Kymmene Oyj Kaukaan kemiallisella tehtaalla. Talloin uutossa saavutettiin noin 50 %:n sterolisaanto. Ultra-sitosterolin laboratoriomittakaavaisissa kiteytyskokeissa vertailtiin neljän eri alkoholin ja kahden muun orgaanisen liuottimen soveltuvuutta kiteytysliuoksen komponenteiksi. Lisaksi tutkittiin vesipitoisuuden liuotinseoksen vaikutusta. Tarkoituksena oli löytää se liuotinkoostumus, jolla sterolikiteiden saanto ja puhtaus olisivat mahdollisimman korkeat. Sopivalla kiteytysliuoksen koostumuksella saavutettiin melko hyvä sterolisaanto ja lähes 98 %:n puhtaus.

Chronic disease management programmes for adults with asthma (intervention Review)

BACKGROUND: The burden of asthma on patients and healthcare systems is substantial. Interventions have been developed to overcome difficulties in asthma management. These include chronic disease management programmes, which are more than simple patient education, encompassing a set of coherent interventions that centre on the patients' needs, encouraging the co-ordination and integration of health services provided by a variety of healthcare professionals, and emphasising patient self-management as well as patient education. OBJECTIVES: To evaluate the effectiveness of chronic disease management programmes for adults with asthma. SEARCH METHODS: Cochrane Central Register of Controlled Trials (CENTRAL), Cochrane Effective Practice and Organisation of Care (EPOC) Group Specialised Register, MEDLINE (MEDLINE In-Process and Other Non-Indexed Citations), EMBASE, CINAHL, and PsycINFO were searched up to June 2014. We also handsearched selected journals from 2000 to 2012 and scanned reference lists of relevant reviews. SELECTION CRITERIA: We included individual or cluster-randomised controlled trials, non-randomised controlled trials, and controlled before-after studies comparing chronic disease management programmes with usual care in adults over 16 years of age with a diagnosis of asthma. The chronic disease management programmes had to satisfy at least the following five criteria: an organisational component targeting patients; an organisational component targeting healthcare professionals or the healthcare system, or both; patient education or self-management support, or both; active involvement of two or more healthcare professionals in patient care; a minimum duration of three months. DATA COLLECTION AND ANALYSIS: After an initial screen of the titles, two review authors working independently assessed the studies for eligibility and study quality; they also extracted the data. We contacted authors to obtain missing information and additional data, where necessary. We pooled results using the random-effects model and reported the pooled mean or standardised mean differences (SMDs). MAIN RESULTS: A total of 20 studies including 81,746 patients (median 129.5) were included in this review, with a follow-up ranging from 3 to more than 12 months. Patients' mean age was 42.5 years, 60% were female, and their asthma was mostly rated as moderate to severe. Overall the studies were of moderate to low methodological quality, because of limitations in their design and the wide confidence intervals for certain results.Compared with usual care, chronic disease management programmes resulted in improvements in asthma-specific quality of life (SMD 0.22, 95% confidence interval (CI) 0.08 to 0.37), asthma severity scores (SMD 0.18, 95% CI 0.05 to 0.30), and lung function tests (SMD 0.19, 95% CI 0.09 to 0.30). The data for improvement in self-efficacy scores were inconclusive (SMD 0.51, 95% CI -0.08 to 1.11). Results on hospitalisations and emergency department or unscheduled visits could not be combined in a meta-analysis because the data were too heterogeneous; results from the individual studies were inconclusive overall. Only a few studies reported results on asthma exacerbations, days off work or school, use of an action plan, and patient satisfaction. Meta-analyses could not be performed for these outcomes. AUTHORS' CONCLUSIONS: There is moderate to low quality evidence that chronic disease management programmes for adults with asthma can improve asthma-specific quality of life, asthma severity, and lung function tests. Overall, these results provide encouraging evidence of the potential effectiveness of these programmes in adults with asthma when compared with usual care. However, the optimal composition of asthma chronic disease management programmes and their added value, compared with education or self-management alone that is usually offered to patients with asthma, need further investigation.

Efecto de ajuste del flujo dializante (Qd) sobre la eficacia en hemodialisis a pacientes de bajo peso

Introducción: Las guías KDOQI del 2006 utilizan patrón de adecuación de diálisis el Kt/V, donde V es volumen de distribución de la úrea, pacientes de bajo peso tienen menor agua corporal total, menor V, que podrían reducir el requerimiento de Qd sin afectar la eficiencia de la diálisis. Objetivo: Evaluar el efecto sobre la adecuación de hemodiálisis que produce la reducción del Qd en pacientes con peso menor o igual a 60 kg . Metodología: Se incluyeron pacientes con Enfermedad Renal crónica en hemodiálisis de forma regular con peso menor o igual a 60 Kg de la unidad renal, para evaluar dos períodos I y II, se continuaron los parámetros de la terapia, con descenso del Qd para el segundo período . Las variables fueron recolectadas de forma directa por los investigadores de la historia clínica . Los valores así obtenidos serían comparados mediante prueba t para variables relacionadas o pareadas, y significancia estadística de la prueba inferior a 0,05. Resultados: Se incluyeron 61 pacientes, el 60.7% sexo femenino, promedio de edad 57,3 años (DE 14,8). Edad promedio de los hombres 60,1 (DE 13,9) y de las mujeres fue de 55,9 (DE 15,4). No se encontraron diferencias estadísticamente significativas para las variables Kt/V y Hb, con descenso significativo del P. (p 0.015) Conclusiones: Este estudio demuestra que se logra una adecuada terapia con Qd inferiores a los estándares tradicionales, con 400ml /min en pacientes de bajo peso, siempre y cuando se mantengan los demás parámetros de suplencia renal.

Efecto del flujo del dializado sobre la ganancia interdialítica en hemodiálisis crónica (Estudio FLUGAIN)

Objetivos: Determinar si existe diferencia en la ganancia interdialítica entre los pacientes al ser tratados con flujo de dializado (Qd) de 400 mL/min y 500 mL/min. Diseño: Se realizó un estudio de intervención, cruzado, aleatorizado, doble ciego en pacientes con enfermedad renal crónica en hemodiálisis para determinar diferencias en la ganancia de peso interdialítica entre los pacientes tratados con flujo de dializado (Qd) de 400 ml/min y 500 ml/min. Pacientes: Se analizaron datos de 46 pacientes en hemodiálisis crónica con Qd de 400 ml/min y 45 con Qd de 500 ml/min. Análisis: La prueba de hipótesis para evaluar diferencias en la ganancia interdialítica y las otras variables entre los grupos se realizó mediante la prueba T para muestras pareadas. Para el análisis de correlación se calculó el coeficiente de Pearson. Resultados: No hubo diferencia significativa en ganancia interdialítica usando Qd de 400 ml/min vs 500 ml/min (2.37 ± 0.7 vs 2.41 ± 0.6, p=0.41) ni en Kt/V (1.57 ± 0.25 vs 1.59 ± 0.23, p = 0.45), potasio (4.9 ± 1.1 vs 5.1 ± 1.0, p=0.45), fosforo (4.5 ± 1.2 vs 4.4 ± 1.2, p=0.56) o hemoglobina (11.3 ± 1.8 vs 11.3 ± 1.6, p=0.96). Conclusiones: En pacientes con peso ≤ 65 Kg el uso de Qd de 400 ml/min no se asocia con menor ganancia interdialítica de peso. No hay diferencia en la eficiencia de diálisis lo que sugiere que es una intervención segura a corto plazo.

Copolimeros de propileno-etileno com baixos teores de etileno : estrutura, morfologia e propriedades

A estrutura básica predomínante encontrada em todos os copolímeros foi a de longos blocos de polipropileno cristalizáveis, separados por unidades isoladas de etileno, que atuaram como defeitos cristalínos, reduzindo o grau de cristalínidade, além da perfeição e da espessura dos cristais. O gradual aumento do teor de etileno nas amostras origínais, até aproximadamente5 moI % provocou redução progressiva no comprimento dos blocos de propileno em ambas as frações cristalizável e elastomérica. Acima daquela concentração, o etileno mostrou por principal efeito a elevação do teor de borracha de etileno-propileno(EPR), refletíndo-seem pronunciado aumento da resistência ao impacto dos copolímeros, com pouca alteração do comprimento das seqüências propiJênicas nas frações cristaJizáveJe elastomérica. A estrutura e a morfologia da borracha EPR gerada foram analisadas, observando-se sua excepcional dispersão na fase contínua cristalína. Análise das curvas de fusão por DSC, utilizando-se conceitos cínéticos, demonstrou a existência de uma energia de ativação aparente de fusão, associada à introdução de unidades etilênicas nas cadeias, e relacionada ao processo de fusão dos cristais poliméricos. A redução de cristalínidade das amostras e o aumento de mobilidade de cadeia da fase amorfa para teores crescentes de etileno resultaram em redução da rigidez dos copolímeros. Propriedades ópticas, como "haze" e brilho mostraram-se dependentesdo balanço entre o teor de cristais e o teor de borracha. Um balanço global das propriedades analisadas sugere uma composição ótima para aplicações típicas de copolímeros de propileno-etileno aquela com teores de etileno entre 4 e 6 moI % (aproximadamente 3 -4 % em massa).

Chemical stability and electrical properties of Nb doped BaCe 0.9Y 0.1O 3-δ as a high temperature proton conducting electrolyte for IT-SOFC

BaCe 0.9-xNb xY 0.1O 3-δ (where x=0, 0.01, 0.03 and 0.05) powders were synthesized by solid-state reaction to investigate the influence of Nb concentration on chemical stability and electrical properties of the sintered samples. The dense electrolyte pellets were formed from the powders after being uniaxially pressed and sintered at 1550 °C. The electrical conductivities determined by impedance measurements in temperature range of 550-750 °C in different atmospheres (dry argon and wet hydrogen) showed a decreasing trend with an increase of Nb content. For all samples higher conductivities were observed in the wet hydrogen than in dry argon atmosphere. The chemical stability was enhanced with increasing of Nb concentration. It was found that BaCe 0.87Nb 0.03Y 0.1O 3-δ is the optimal composition that satisfies the opposite demands for electrical conductivity and chemical stability, reaching 0.8×10 -2 S cm -1 in wet hydrogen at 650 °C compared to 1.01×10 -2 S cm -1 for undoped electrolyte. © 2012 Elsevier Ltd and Techna Group S.r.l.

Liquid lead and Lithium. A Comprehensive molecular dynamics study

Pb17Li is today a reference breeder material in diverse fusion R&D programs worldwide. One of the main issues in these programs is the problem of liquid metals breeder blanket behavior. Structural material of the blanket should meet high requirements because of extreme operating conditions. Therefore the knowledge of eutectic properties like optimal composition, physical and thermodynamic behavior or diffusion coefficients of Tritium are extremely necessary for current designs. In particular, the knowledge of the function linking the tritium concentration dissolved in liquid materials with the tritium partial pressure at a liquid/gas interface in equilibrium, CT=f(PT), is of basic importance because it directly impacts all functional properties of a blanket determining: tritium inventory, tritium permeation rate and tritium extraction efficiency. Nowadays, understanding the structure and behavior of this compound is a real goal in fusion engineering and materials science. Simulations of liquids can provide much information to the community; not only supplementing experimental data, but providing new tests of theories and ideas, making specific predictions that require experimental tests, and ultimately helping to lead to the deeper understanding and better predictive behavior.

New simulations to qualify eutectic lithium-lead as breeder material

Pb17Li is today a reference breeder material in diverse fusion R&D programs worldwide. One of the main issues is the problem of liquid metals breeder blanket behavior. The knowledge of eutectic properties like optimal composition, physical and thermodynamic behavior or diffusion coefficients of Tritium are extremely necessary for current designs. In particular, the knowledge of the function linking the tritium concentration dissolved in liquid materials with the tritium partial pressure at a liquid/gas interface in equilibrium, CT =f(PT ), is of basic importance because it directly impacts all functional properties of a blanket determining: tritium inventory, tritium permeation rate and tritium extraction efficiency. Nowadays, understanding the structure and behavior of this compound is a real goal in fusion engineering and materials science. Atomistic simulations of liquids can provide much information; not only supplementing experimental data, but providing new tests of theories and ideas, making specific predictions that require experimental tests, and ultimately helping to a deeper understanding

The role of glass modifiers in the solubility of Tm3+ ions in As2S3 glasses

Au cours des années une variété des compositions de verre chalcogénure a été étudiée en tant qu’une matrice hôte pour les ions Terres Rares (TR). Pourtant, l’obtention d’une matrice de verre avec une haute solubilité des ions TR et la fabrication d’une fibre chalcogénure dopée au TR avec une bonne qualité optique reste toujours un grand défi. La présente thèse de doctorat se concentre sur l’étude de nouveaux systèmes vitreux comme des matrices hôtes pour le dopage des ions TR, ce qui a permis d’obtenir des fibres optiques dopées au TR qui sont transparents dans l’IR proche et moyenne. Les systèmes vitreux étudiés ont été basés sur le verre de sulfure d’arsenic (As2S3) co-dopé aux ions de Tm3+ et aux différents modificateurs du verre. Premièrement, l’addition de Gallium (Ga), comme un co-dopant, a été examinée et son influence sur les propriétés d’émission des ions de Tm a été explorée. Avec l’incorporation de Ga, la matrice d’As2S3 dopée au Tm a montré trois bandes d’émission à 1.2 μm (1H5→3H6), 1.4 μm (3H4→3F4) et 1.8 μm (3F4→3H6), sous l’excitation des longueurs d’onde de 698 nm et 800 nm. Les concentrations de Tm et de Ga ont été optimisées afin d’obtenir le meilleur rendement possible de photoluminescence. À partir de la composition optimale, la fibre Ga-As-S dopée au Tm3+ a été étirée et ses propriétés de luminescence ont été étudiées. Un mécanisme de formation structurale a été proposé pour ce système vitreux par la caractérisation structurale des verres Ga-As-S dopés au Tm3+, en utilisant la spectroscopie Raman et l’analyse de spectrométrie d’absorption des rayons X (EXAFS) à seuil K d’As, seuil K de Ga et seuil L3 de Tm et il a été corrélé avec les caractéristiques de luminescence de Tm. Dans la deuxième partie, la modification des verres As2S3 dopés au Tm3+, avec l’incorporation d’halogénures (Iode (I2)), a été étudiée en tant qu’une méthode pour l’adaptation des paramètres du procédé de purification afin d’obtenir une matrice de verre de haute pureté par distillation chimique. Les trois bandes d’émission susmentionnées ont été aussi bien observées pour ce système sous l’excitation à 800 nm. Les propriétés optiques, thermiques et structurelles de ces systèmes vitreux ont été caractérisées expérimentalement en fonction de la concentration d’I2 et de Tm dans le verre, où l’attention a été concentrée sur deux aspects principaux: l’influence de la concentration d’I2 sur l’intensité d’émission de Tm et les mécanismes responsables pour l’augmentation de la solubilité des ions de Tm dans la matrice d’As2S3 avec l’addition I2.

The composition of mineral waters sourced from Europe and North America in respect to bone health: composition of mineral water optimal for bone.

The consumption of mineral waters is increasing in industrialised countries. High intakes of Ca and other alkalising cations as well as a low acid intake are beneficial to bone. We examined which components of mineral waters are conditioning their Ca content and their alkalinising power, in order to define the optimal profile. European mineral waters were randomly selected on the Internet: 100 waters with less than 200 mg Ca/l (9.98 mEq/l) and fifty with more than 200 mg/l, all with complete data for SO4, P, Cl, Na, K, Mg and Ca, and most also for HCO3. For comparison, forty North American mineral waters were randomly chosen. The potential renal acid load (PRAL) was calculated for each mineral water. North American waters did not reveal significant results because of their low mineralisation. We performed correlations between all eight components in order to explore the properties of the mineral waters. In the European waters, twenty-six out of twenty-eight correlations showed a P value of <or= 0.01. In waters with PRAL >0 (acidifying waters), PRAL was positively correlated with SO4, Ca, K and Mg (P < 0.001). In those with PRAL < 0 (alkalinising waters), PRAL was negatively correlated with HCO3, Na, Mg, Ca, K, Cl and SO4 (P < 0.001). SO4 and HCO3 were not found together in high quantities in the same water for geochemical reasons. A high Ca content is associated with either a high SO4 or a high HCO3 content. SO4 theoretically increases Ca excretion, while HCO3 and low PRAL values are associated with positive effects on bone. Therefore, the best waters for bone health are rich in both HCO3 and Ca, and by consequence low in SO4.

Genetic team composition and level of selection in the evolution of cooperation

In cooperative multiagent systems, agents interac to solve tasks. Global dynamics of multiagent teams result from local agent interactions, and are complex and difficult to predict. Evolutionary computation has proven a promising approach to the design of such teams. The majority of current studies use teams composed of agents with identical control rules ("geneti- cally homogeneous teams") and select behavior at the team level ("team-level selection"). Here we extend current approaches to include four combinations of genetic team composition and level of selection. We compare the performance of genetically homo- geneous teams evolved with individual-level selection, genetically homogeneous teams evolved with team-level selection, genetically heterogeneous teams evolved with individual-level selection, and genetically heterogeneous teams evolved with team-level selection. We use a simulated foraging task to show that the optimal combination depends on the amount of cooperation required by the task. Accordingly, we distinguish between three types of cooperative tasks and suggest guidelines for the optimal choice of genetic team composition and level of selection

Appropriate IPRs, Human Capital Composition and Economic Growth

We generalize a standard technology diffusion model by allowing for IPRs regimes to be endogenously defined by the development level of each country. Also we insert differences in the composition of human capital between North (leader) and South (followers) which shape the relative costs of innovation and imitation. Results show how an optimal growth trajectory is found for the follower country which initially imitates and that, once a "threshold development stage" is reached, optimally switches to innovation by fully enforcing IPRs achieving a higher proximity with the technology frontier in the long-run. Other scenarios, such as a premature increase in the enforcement of IPRs or a switch from imitation to innovation at early stages of development of the followers are found to be sub-optimal.

Optimal Recycling Combination of Ash in South-East Finland

The present world energy production is heavily relying on the combustion of solid fuels like coals, peat, biomass, municipal solid waste, whereas the share of renewable fuels is anticipated to increase in the future to mitigate climate change. In Finland, peat and wood are widely used for energy production. In any case, the combustion of solid fuels results in generation of several types of thermal conversion residues, such as bottom ash, fly ash, and boiler slag. The predominant residue type is determined by the incineration technology applied, while its composition is primarily relevant to the composition of fuels combusted. An extensive research has been conducted on technical suitability of ash for multiple recycling methods. Most of attention was drawn to the recycling of the coal combustion residues, as coal is the primary solid fuel consumed globally. The recycling methods of coal residues include utilization in a cement industry, in concrete manufacturing, and mine backfilling, to name few. Biomass combustion residues were also studied to some extent with forest fertilization, road construction, and road stabilization being the predominant utilization options. Lastly, residues form municipal solid waste incineration attracted more attention recently following the growing number of waste incineration plants globally. The recycling methods of waste incineration residues are the most limited due to its hazardous nature and varying composition, and include, among others, landfill construction, road construction, mine backfilling. In the study, environmental and economic aspects of multiple recycling options of thermal conversion residues generated within a case-study area were studied. The case-study area was South-East Finland. The environmental analysis was performed using an internationally recognized methodology — life cycle assessment. Economic assessment was conducted applying a widely used methodology — cost-benefit analysis. Finally, the results of the analyses were combined to enable easier comparison of the recycling methods. The recycling methods included the use of ash in forest fertilization, road construction, road stabilization, and landfill construction. Ash landfilling was set as a baseline scenario. Quantitative data about the amounts of ash generated and its composition was obtained from companies, their environmental reports, technical reports and other previously published literature. Overall, the amount of ash in the case-study area was 101 700 t. However, the data about 58 400 t of fly ash and 35 100 t of bottom ash and boiler slag were included in the study due to lack of data about leaching of heavy metals in some cases. The recycling methods were modelled according to the scientific studies published previously. Overall, the results of the study indicated that ash utilization for fertilization and neutralization of 17 600 ha of forest was the most economically beneficial method, which resulted in the net present value increase by 58% compared to ash landfilling. Regarding the environmental impact, the use of ash in the construction of 11 km of roads was the most attractive method with decreased environmental impact of 13% compared to ash landfilling. The least preferred method was the use of ash for landfill construction since it only enabled 11% increase of net present value, while inducing additional 1% of negative impact on the environment. Therefore, a following recycling route was proposed in the study. Where possible and legally acceptable, recycle fly and bottom ash for forest fertilization, which has strictest requirements out of all studied methods. If the quality of fly ash is not suitable for forest fertilization, then it should be utilized, first, in paved road construction, second, in road stabilization. Bottom ash not suitable for forest fertilization, as well as boiler slag, should be used in landfill construction. Landfilling should only be practiced when recycling by either of the methods is not possible due to legal requirements or there is not enough demand on the market. Current demand on ash and possible changes in the future were assessed in the study. Currently, the area of forest fertilized in the case-study are is only 451 ha, whereas about 17 600 ha of forest could be fertilized with ash generated in the region. Provided that the average forest fertilizing values in Finland are higher and the area treated with fellings is about 40 000 ha, the amount of ash utilized in forest fertilization could be increased. Regarding road construction, no new projects launched by the Center of Economic Development, Transport and the Environment in the case-study area were identified. A potential application can be found in the construction of private roads. However, no centralized data about such projects is available. The use of ash in stabilization of forest roads is not expected to increased in the future with a current downwards trend in the length of forest roads built. Finally, the use of ash in landfill construction is not a promising option due to the reducing number of landfills in operation in Finland.