Inverse Metabolic Engineering of Synechocystis PCC 6803 for Improved Growth Rate and Poly-3-hydroxybutyrate Production

Synechocystis PCC 6803 is a photosynthetic bacterium that has the potential to make bioproducts from carbon dioxide and light. Biochemical production from photosynthetic organisms is attractive because it replaces the typical bioprocessing steps of crop growth, milling, and fermentation, with a one-step photosynthetic process. However, low yields and slow growth rates limit the economic potential of such endeavors. Rational metabolic engineering methods are hindered by limited cellular knowledge and inadequate models of Synechocystis. Instead, inverse metabolic engineering, a scheme based on combinatorial gene searches which does not require detailed cellular models, but can exploit sequence data and existing molecular biological techniques, was used to find genes that (1) improve the production of the biopolymer poly-3-hydroxybutyrate (PHB) and (2) increase the growth rate. A fluorescence activated cell sorting assay was developed to screen for high PHB producing clones. Separately, serial sub-culturing was used to select clones that improve growth rate. Novel gene knock-outs were identified that increase PHB production and others that increase the specific growth rate. These improvements make this system more attractive for industrial use and demonstrate the power of inverse metabolic engineering to identify novel phenotype-associated genes in poorly understood systems.

Constitutional judges (guarantee of the Constitution and responsibility)

My aim in this paper is to propose a reflection on the position and the importance that the constitutional judge has in the legal systems of contemporary constitutionalism. The figure of the judge responsible of protecting the Constitution is a key institution, without which we cannot understand the laws of constitutional democracies, their current lines of development, and the guarantee of rights and freedoms that constitute the normative core of these systems. Moreover, the reflection on the exercise of the powers of the judge, its scope and its justification is an important part of contemporary legal discussion, still relevant, albeit not exclusively - in the field of legal philosophy. The object of attention of my reflection is the judge who has the power of judicial review, in a scheme of defense of the Constitution, regardless the specific ways of this defense.

Combatant recruitment and the outcome of war

Why do some civil wars terminate soon, with victory of one party over the other? What determines if the winner is the incumbent or the rebel group? Why do other conáicts last longer? We propose a simple model in which the power of each armed group depends on the number of combatants it is able to recruit. This is in turn a function of the relative ëdistanceíbetween group leaderships and potential recruits. We emphasize the moral hazard problem of recruitment: Öghting is costly and risky so combatants have the incentive to defect from their task. They can also desert altogether and join the enemy. This incentive is stronger the farther away the Öghter is from the principal, since monitoring becomes increasingly costly. Bigger armies have more power but less monitoring capacity to prevent defection and desertion. This general framework allows a variety of interpretations of what type of proximity matters for building strong cohesive armies ranging from ethnic distance to geographic dispersion. Di§erent assumptions about the distribution of potential Öghters along the relevant dimension of conáict lead to di§erent equilibria. We characterize these, discuss the implied outcome in terms of who wins the war, and illustrate with historical and contemporaneous case studies.

Does uncertainty cause inertia in decision making? An experimental study of the role of regret aversion and indecisiveness

Previous research has shown that often there is clear inertia in individual decision making---that is, a tendency for decision makers to choose a status quo option. I conduct a laboratory experiment to investigate two potential determinants of inertia in uncertain environments: (i) regret aversion and (ii) ambiguity-driven indecisiveness. I use a between-subjects design with varying conditions to identify the effects of these two mechanisms on choice behavior. In each condition, participants choose between two simple real gambles, one of which is the status quo option. I find that inertia is quite large and that both mechanisms are equally important.

Comparing meta-analysis and ecological-longitudinal analysis in time-series studies: a case study of the effects of air pollution on mortality in three Spanish cities

The objective of this paper is to introduce a diVerent approach, called the ecological-longitudinal, to carrying out pooled analysis in time series ecological studies. Because it gives a larger number of data points and, hence, increases the statistical power of the analysis, this approach, unlike conventional ones, allows the complementation of aspects such as accommodation of random effect models, of lags, of interaction between pollutants and between pollutants and meteorological variables, that are hardly implemented in conventional approaches. Design—The approach is illustrated by providing quantitative estimates of the short-termeVects of air pollution on mortality in three Spanish cities, Barcelona,Valencia and Vigo, for the period 1992–1994. Because the dependent variable was a count, a Poisson generalised linear model was first specified. Several modelling issues are worth mentioning. Firstly, because the relations between mortality and explanatory variables were nonlinear, cubic splines were used for covariate control, leading to a generalised additive model, GAM. Secondly, the effects of the predictors on the response were allowed to occur with some lag. Thirdly, the residual autocorrelation, because of imperfect control, was controlled for by means of an autoregressive Poisson GAM. Finally, the longitudinal design demanded the consideration of the existence of individual heterogeneity, requiring the consideration of mixed models. Main results—The estimates of the relative risks obtained from the individual analyses varied across cities, particularly those associated with sulphur dioxide. The highest relative risks corresponded to black smoke in Valencia. These estimates were higher than those obtained from the ecological-longitudinal analysis. Relative risks estimated from this latter analysis were practically identical across cities, 1.00638 (95% confidence intervals 1.0002, 1.0011) for a black smoke increase of 10 μg/m3 and 1.00415 (95% CI 1.0001, 1.0007) for a increase of 10 μg/m3 of sulphur dioxide. Because the statistical power is higher than in the individual analysis more interactions were statistically significant,especially those among air pollutants and meteorological variables. Conclusions—Air pollutant levels were related to mortality in the three cities of the study, Barcelona, Valencia and Vigo. These results were consistent with similar studies in other cities, with other multicentric studies and coherent with both, previous individual, for each city, and multicentric studies for all three cities

Predictors of knowledge creation performance. A quantitative qualitative comparative study of European doctorandi

Aquesta tesi forma part d'un projecte destinat a predir el rendiment acadèmic dels estudiants de doctorat portat a terme per l'INSOC (International Network on Social Capital and Performance). El grup de recerca INSOC està format per les universitats de Girona (Espanya), Ljubljana (Eslovènia), Giessen (Alemanya) i Ghent (Bèlgica). El primer objectiu d'aquesta tesi és desenvolupar anàlisis quantitatius comparatius sobre el rendiment acadèmic dels estudiants de doctorat entre Espanya, Eslovènia i Alemanya a partir dels resultats individuals del rendiment acadèmic obtinguts de cada una de les universitats. La naturalesa internacional del grup de recerca implica la recerca comparativa. Vam utilitzar variables personal, actitudinals i de xarxa per predir el rendiment. El segon objectiu d'aquesta tesi és entendre de manera qualitativa perquè les variables de xarxa no ajuden quantitativament a predir el rendiment a la universitat de Girona (Espanya). En el capítol 1, definim conceptes relacionats amb el rendiment i donam un llistat de cada una de les variables independents (variables de xarxa, personals i actitudinals), resumint la lliteratura. Finalment, explicam com s'organitzen els estudis de doctorat a cada un dels diferents països. A partir d'aquestes definicions teòriques, en els pròxims capítols, primer presentarem els qüestionaris utilitzats a Espanya, Eslovènia i Alemanya per mesurar aquests diferents tipus de variables. Després, compararem les variables que són relevants per predir el rendiment dels estudiants de doctorat a cada país. Després d'això, fixarem diferents models de regressió per predir el rendiment entre països. En tots aquests models les variables de xarxa fallen a predir el rendiment a la Universitat de Girona. Finalment, utilitzem estudis qualitatius per entendre aquests resultats inesperats. En el capítol 2, expliquem com hem dissenyat i conduït els qüestionaris en els diferents països amb l'objectiu d'explicar el rendiment dels estudiants de doctorat obtinguts a Espanya, Eslovènia i Alemanya. En el capítol 3, cream indicadors comparables però apareixen problemes de comparabilitat en preguntes particulars a Espanya, Eslovènia i Alemanya. En aquest capítol expliquem com utilitzem les variables dels tres països per crear indicadors comparables. Aquest pas és molt important perquè el principal objectiu del grup de recerca INSOC és comparar el rendiment dels estudiants de doctorat entre els diferents països. En el capítol 4 comparem models de regressió obtinguts de predir el rendiment dels estudiants de doctorat a les universitats de Girona (Espanya) i Eslovènia. Les variables són característiques dels grups de recerca dels estudiants de doctorat enteses com una xarxa social egocèntrica, característiques personals i actitudinals dels estudiants de doctorat i algunes carecterístiques dels directors. Vam trobar que les variables de xarxa egocèntriques no predien el rendiment a la Universitat de Girona. En el capítol 5, comparem dades eslovenes, espanyoles i alemnayes, seguint la metodologia del capítol 4. Concluïm que el cas alemany és molt diferent. El poder predictiu de les variables de xarxa no millora. En el capítol 6 el grup de recerca dels estudiants de doctorat és entès com una xarxa duocèntrica (Coromina et al., 2008), amb l'objectiu d'obtendre informació de la relació mútua entre els estudiants i els seus directors i els contactes d'ambdós amb els altres de la xarxa. La inclusió de la xarxa duocèntrica no millora el poder predictiu del model de regressió utilitzant les variales egocèntriques de xarxa. El capítol 7 pretèn entendre perquè les variables de xarxa no predeixen el rendiment a la Universitat de Girona. Utilitzem el mètode mixte, esperant que l'estudi qualitatiu pugui cobrir les raons de perquè la qualitat de la xarxa falla en la qualitat del treball dels estudiants. Per recollir dades per l'estudi qualitatiu utilitzem entrevistes en profunditat.

Elizabeth Bishop’s sounds of sanity

In this article, I examine the implications of rewriting definitions of sanity and insanity through the use of noise, silence, and language,positioningElizabeth Bishop’s short story “In the Village” as a form of resistance against traditional readings of madness, logocentrism, and identity. I suggest that by writing her characters as undivided from the world of sound, Elizabeth Bishop’s story shifts understandings of insanity, which is often conceptualized through denials of agency, allowing her characters to escape in noises and hesitations in language and communication. “In the Village” avoids silencing the “insane” mother through her placement in a caesura of sound and silence. This article avoids a biographical reading of “In the Village,” which is often connected with her own mother’s “mental breakdown,” because Bishop’s writing would have been as much affected by her conscious awareness of her past as it was by the unconscious impulses and histories of writing in the West. Rather, I take into account Bishop’s own personal history as well as the repetitions that reflect a placement in a tradition appearing in the story itself. Using this particular lens, I believe a rereading of “In the Village” is in order, where the “mad mother” is not silenced by the oppressive social structures that control the insane,” but she instead finds escape in the multitudes of sounds that associate with her, erasing the power of language and opening a new world where agency exists in a scream or in a striking hammer.

"Ella", de Juan Carlos Onetti. Necrofilia y ficción (Homenaje)

La autora reflexiona sobre el relato “Ella”, del uruguayo Juan Carlos Onetti, y sobre otras representaciones de la muerte de Eva Perón, escritas por Jorge Luis Borges, David Viñas y Néstor Perlongher. Afirma que en la Argentina de Perón ya confluían realidad y ficción, y que las múltiples biografías de Eva serían “un duelo de versiones narrativas entre la ficción y la historia o, si se prefiere, una metáfora de la historia”. Rosano plantea que, en los textos revisados, es la realidad la que adopta contornos fantasmagóricos, disparados por motivos diversos: la descomposición y el tópico del mal olor, la impostura del cuerpo embalsamado y del mandatario, el entrelazamiento entre lo político y lo sexual en la escena del velorio, la imagen de Eva, “una diosa que muestra sus encajes de novia de suburbio” pero también una siniestra y doliente “zombi escarlata”. Señala, finalmente, que los textos muestran a los fieles, esos “miles de necrófilos murmurantes y enlutados”, sometidos a la potencia del mito.

The post-Lisbon role of the European Parliament in the EU's Common Commercial Policy: Implications for bilateral trade negotiations. EU Diplomacy Paper 05/2012, July 2012

This paper sets out to conduct an empirical analysis of the post-Lisbon role of the European Parliament (EP) in the EU’s Common Commercial Policy through an examination of the ‘deep and comprehensive’ bilateral Free Trade Agreements (FTAs) currently negotiated as part of the EU’s Global Europe strategy. The EU-Korea and EU-India FTAs are used as case studies in order to determine the implications of the EP’s enhanced trade powers on the processes, actors and outcomes of EU bilateral trade policy. The EP is now endowed with the ‘hard power’ of consent in the ratification phase of FTAs, acting as a threat to strengthen its ‘soft power’ to influence negotiations. The EP is developing strategies to influence the mandate and now plays an important role in the implementation of FTAs. The entry of this new player on the Brussels trade policy field has brought about a shift in the institutional balance of power and opened up the EP as a new point of access for trade policy lobbyists. Finally, increased EP involvement in EU trade policy has brought about a politicisation of EU trade policy and greater normative outcomes of FTAs.

Vibration-rotation spectra of CH3F

Rotational structure has been resolved and analyzed in the 1049-cm−1 parallel fundamental and the 1182 cm−1 perpendicular fundamental bands in the infrared spectrum of the CH3F molecule. Combination bands at 2223 cm−1 and around 2650 cm−1 have also been studied. The effective resolving power of the spectrometer was 0.25 cm−1 for all these bands. The two long-wavelength fundamentals have been analyzed in much greater detail than in previous work, and a complete analysis of the perpendicular band has been made, including the J-structure in the P and R branches of the sub-bands. Rotational constants of CH3F determined in this work and elsewhere are summarized in Table XIII of the text. Some anomalous intensity perturbations in the rotation lines of the 1182-cm−1 fundamental have been observed, and are discussed.

Mathematical modelling of decision making processes in construction projects

Many different individuals, who have their own expertise and criteria for decision making, are involved in making decisions on construction projects. Decision-making processes are thus significantly affected by communication, in which a dynamic performance of human intentions leads to unpredictable outcomes. In order to theorise the decision making processes including communication, it is argued here that the decision making processes resemble evolutionary dynamics in terms of both selection and mutation, which can be expressed by the replicator-mutator equation. To support this argument, a mathematical model of decision making has been made from an analogy with evolutionary dynamics, in which there are three variables: initial support rate, business hierarchy, and power of persuasion. On the other hand, a survey of patterns in decision making in construction projects has also been performed through self-administered mail questionnaire to construction practitioners. Consequently, comparison between the numerical analysis of mathematical model and the statistical analysis of empirical data has shown a significant potential of the replicator-mutator equation as a tool to study dynamic properties of intentions in communication.

Estimating technical efficiency of Australian dairy farms using alternative frontier methodologies

Technical efficiency is estimated and examined for a cross-section of Australian dairy farms using various frontier methodologies; Bayesian and Classical stochastic frontiers, and Data Envelopment Analysis. The results indicate technical inefficiency is present in the sample data. Also identified are statistical differences between the point estimates of technical efficiency generated by the various methodologies. However, the rank of farm level technical efficiency is statistically invariant to the estimation technique employed. Finally, when confidence/credible intervals of technical efficiency are compared significant overlap is found for many of the farms' intervals for all frontier methods employed. The results indicate that the choice of estimation methodology may matter, but the explanatory power of all frontier methods is significantly weaker when interval estimate of technical efficiency is examined.

Statistical design and analysis of pharmacogenetic trials

Pharmacogenetic trials investigate the effect of genotype on treatment response. When there are two or more treatment groups and two or more genetic groups, investigation of gene-treatment interactions is of key interest. However, calculation of the power to detect such interactions is complicated because this depends not only on the treatment effect size within each genetic group, but also on the number of genetic groups, the size of each genetic group, and the type of genetic effect that is both present and tested for. The scale chosen to measure the magnitude of an interaction can also be problematic, especially for the binary case. Elston et al. proposed a test for detecting the presence of gene-treatment interactions for binary responses, and gave appropriate power calculations. This paper shows how the same approach can also be used for normally distributed responses. We also propose a method for analysing and performing sample size calculations based on a generalized linear model (GLM) approach. The power of the Elston et al. and GLM approaches are compared for the binary and normal case using several illustrative examples. While more sensitive to errors in model specification than the Elston et al. approach, the GLM approach is much more flexible and in many cases more powerful. Copyright © 2005 John Wiley & Sons, Ltd.

A practical comparison of group-sequential and adaptive designs

Sequential methods provide a formal framework by which clinical trial data can be monitored as they accumulate. The results from interim analyses can be used either to modify the design of the remainder of the trial or to stop the trial as soon as sufficient evidence of either the presence or absence of a treatment effect is available. The circumstances under which the trial will be stopped with a claim of superiority for the experimental treatment, must, however, be determined in advance so as to control the overall type I error rate. One approach to calculating the stopping rule is the group-sequential method. A relatively recent alternative to group-sequential approaches is the adaptive design method. This latter approach provides considerable flexibility in changes to the design of a clinical trial at an interim point. However, a criticism is that the method by which evidence from different parts of the trial is combined means that a final comparison of treatments is not based on a sufficient statistic for the treatment difference, suggesting that the method may lack power. The aim of this paper is to compare two adaptive design approaches with the group-sequential approach. We first compare the form of the stopping boundaries obtained using the different methods. We then focus on a comparison of the power of the different trials when they are designed so as to be as similar as possible. We conclude that all methods acceptably control type I error rate and power when the sample size is modified based on a variance estimate, provided no interim analysis is so small that the asymptotic properties of the test statistic no longer hold. In the latter case, the group-sequential approach is to be preferred. Provided that asymptotic assumptions hold, the adaptive design approaches control the type I error rate even if the sample size is adjusted on the basis of an estimate of the treatment effect, showing that the adaptive designs allow more modifications than the group-sequential method.

A novel parallel approach to the likelihood-based estimation of admixture in population genetics

Inferring population admixture from genetic data and quantifying it is a difficult but crucial task in evolutionary and conservation biology. Unfortunately state-of-the-art probabilistic approaches are computationally demanding. Effectively exploiting the computational power of modern multiprocessor systems can thus have a positive impact to Monte Carlo-based simulation of admixture modeling. A novel parallel approach is briefly described and promising results on its message passing interface (MPI)-based C implementation are reported.