Use of a short hPDE6b promoter for rod gene transfer in a model of severe retinal cystrophy, the Rd10 mouse

Purpose: Gene therapy of severe retinal dystrophies directly affecting photoreceptor is still a challenge in terms of clinical application. One of the main hurdles is to generate high transgene expression specifically in rods or cones. In the present study, we are investigating the possibility to drive hPDE6b expression in the Rd10 mouse retina using a specific sequence of the human PDE6b promoter. Methods: Two 5' flanking fragments of the human PDE6b gene: (-93 to +53 (146 bp) and -297 to +53 (350 bp, see Di Polo and Farber, 1995) were cloned in different plasmids in order to check their expression in vitro and in vivo. These elements drove the activity of either luciferase (pGL3 plasmids) or EGFP (AAV2/8 backbone). Then, an AAV2/8 vector carrying the PDE6b cDNA was tested with subretinal injections at P9 in the Rd10 eyes. Eye fundus, OCT, ERG recordings and histological investigations were performed to assess the efficacy of the gene transfer. Results: The short PDE6b promoter containing 146bp (-93 to +53) showed the highest activity in the Y-79 cells, as described previously (Di Polo and Farber, 1995). Subretinal administrations of AAV2/8-PDE6bpromoter-EGFP allowed a rapid expression specifically in rods and not in cones. The expression is faster than a vector containing the CMV promoter. The AAV2/8-PDE6bpromoter-PDE6b and the control vector were injected at P9 in the Rd10 mouse retina and investigated 5 weeks post-injection. Out of 14 eyes, 6 presented an increased rod sensitivity of about 300 fold, and increased a- and b-wave responses in ERG recordings. Flicker stimulations revealed that cones are also functional. OCT images and histological analyses revealed an increased ONL size in the injected area. The retina treated with the therapeutic vector presented 4-6 rows of photoreceptors with outersegments containing PDE6b. In the control eyes, only 2-4 rows of photoreceptors with almost no OS were observed . Conclusions: The 146 bp promoter sequence (-93 to + 53) is the shortest regulatory element described to date which allows to obtain efficient rod-specific expression in the context of somatic gene transfer. This first result is of great interest for AAV vector design in general allowing more space for the accommodation of transgenes of interest and good expression in rods. Moreover we showed the proof of principle of the efficacy of AAV2/8-PDE6bp-PDE6b vector in the Rd10 mouse model of severe photoreceptor degeneration without using neither AAV mutated capsids, nor self-complementary vectors.

Minimizing recombinations in consensus networks for phylogeographic studies

Background: We address the problem of studying recombinational variations in (human) populations. In this paper, our focus is on one computational aspect of the general task: Given two networks G1 and G2, with both mutation and recombination events, defined on overlapping sets of extant units the objective is to compute a consensus network G3 with minimum number of additional recombinations. We describe a polynomial time algorithm with a guarantee that the number of computed new recombination events is within ϵ = sz(G1, G2) (function sz is a well-behaved function of the sizes and topologies of G1 and G2) of the optimal number of recombinations. To date, this is the best known result for a network consensus problem.Results: Although the network consensus problem can be applied to a variety of domains, here we focus on structure of human populations. With our preliminary analysis on a segment of the human Chromosome X data we are able to infer ancient recombinations, population-specific recombinations and more, which also support the widely accepted 'Out of Africa' model. These results have been verified independently using traditional manual procedures. To the best of our knowledge, this is the first recombinations-based characterization of human populations. Conclusion: We show that our mathematical model identifies recombination spots in the individual haplotypes; the aggregate of these spots over a set of haplotypes defines a recombinational landscape that has enough signal to detect continental as well as population divide based on a short segment of Chromosome X. In particular, we are able to infer ancient recombinations, population-specific recombinations and more, which also support the widely accepted 'Out of Africa' model. The agreement with mutation-based analysis can be viewed as an indirect validation of our results and the model. Since the model in principle gives us more information embedded in the networks, in our future work, we plan to investigate more non-traditional questions via these structures computed by our methodology.

Full diversity product codes for block erasure and block fading channels

We show how to build full-diversity product codes under both iterative encoding and decoding over non-ergodic channels, in presence of block erasure and block fading. The concept of a rootcheck or a root subcode is introduced by generalizing the same principle recently invented for low-density parity-check codes. We also describe some channel related graphical properties of the new family of product codes, a familyreferred to as root product codes.

Evolving from inferences to decisions in the interpretation of scientific evidence

Le travail d'un(e) expert(e) en science forensique exige que ce dernier (cette dernière) prenne une série de décisions. Ces décisions sont difficiles parce qu'elles doivent être prises dans l'inévitable présence d'incertitude, dans le contexte unique des circonstances qui entourent la décision, et, parfois, parce qu'elles sont complexes suite à de nombreuse variables aléatoires et dépendantes les unes des autres. Etant donné que ces décisions peuvent aboutir à des conséquences sérieuses dans l'administration de la justice, la prise de décisions en science forensique devrait être soutenue par un cadre robuste qui fait des inférences en présence d'incertitudes et des décisions sur la base de ces inférences. L'objectif de cette thèse est de répondre à ce besoin en présentant un cadre théorique pour faire des choix rationnels dans des problèmes de décisions rencontrés par les experts dans un laboratoire de science forensique. L'inférence et la théorie de la décision bayésienne satisfont les conditions nécessaires pour un tel cadre théorique. Pour atteindre son objectif, cette thèse consiste de trois propositions, recommandant l'utilisation (1) de la théorie de la décision, (2) des réseaux bayésiens, et (3) des réseaux bayésiens de décision pour gérer des problèmes d'inférence et de décision forensiques. Les résultats présentent un cadre uniforme et cohérent pour faire des inférences et des décisions en science forensique qui utilise les concepts théoriques ci-dessus. Ils décrivent comment organiser chaque type de problème en le décomposant dans ses différents éléments, et comment trouver le meilleur plan d'action en faisant la distinction entre des problèmes de décision en une étape et des problèmes de décision en deux étapes et en y appliquant le principe de la maximisation de l'utilité espérée. Pour illustrer l'application de ce cadre à des problèmes rencontrés par les experts dans un laboratoire de science forensique, des études de cas théoriques appliquent la théorie de la décision, les réseaux bayésiens et les réseaux bayésiens de décision à une sélection de différents types de problèmes d'inférence et de décision impliquant différentes catégories de traces. Deux études du problème des deux traces illustrent comment la construction de réseaux bayésiens permet de gérer des problèmes d'inférence complexes, et ainsi surmonter l'obstacle de la complexité qui peut être présent dans des problèmes de décision. Trois études-une sur ce qu'il faut conclure d'une recherche dans une banque de données qui fournit exactement une correspondance, une sur quel génotype il faut rechercher dans une banque de données sur la base des observations faites sur des résultats de profilage d'ADN, et une sur s'il faut soumettre une trace digitale à un processus qui compare la trace avec des empreintes de sources potentielles-expliquent l'application de la théorie de la décision et des réseaux bayésiens de décision à chacune de ces décisions. Les résultats des études des cas théoriques soutiennent les trois propositions avancées dans cette thèse. Ainsi, cette thèse présente un cadre uniforme pour organiser et trouver le plan d'action le plus rationnel dans des problèmes de décisions rencontrés par les experts dans un laboratoire de science forensique. Le cadre proposé est un outil interactif et exploratoire qui permet de mieux comprendre un problème de décision afin que cette compréhension puisse aboutir à des choix qui sont mieux informés. - Forensic science casework involves making a sériés of choices. The difficulty in making these choices lies in the inévitable presence of uncertainty, the unique context of circumstances surrounding each décision and, in some cases, the complexity due to numerous, interrelated random variables. Given that these décisions can lead to serious conséquences in the admin-istration of justice, forensic décision making should be supported by a robust framework that makes inferences under uncertainty and décisions based on these inferences. The objective of this thesis is to respond to this need by presenting a framework for making rational choices in décision problems encountered by scientists in forensic science laboratories. Bayesian inference and décision theory meets the requirements for such a framework. To attain its objective, this thesis consists of three propositions, advocating the use of (1) décision theory, (2) Bayesian networks, and (3) influence diagrams for handling forensic inference and décision problems. The results present a uniform and coherent framework for making inferences and décisions in forensic science using the above theoretical concepts. They describe how to organize each type of problem by breaking it down into its différent elements, and how to find the most rational course of action by distinguishing between one-stage and two-stage décision problems and applying the principle of expected utility maximization. To illustrate the framework's application to the problems encountered by scientists in forensic science laboratories, theoretical case studies apply décision theory, Bayesian net-works and influence diagrams to a selection of différent types of inference and décision problems dealing with différent catégories of trace evidence. Two studies of the two-trace problem illustrate how the construction of Bayesian networks can handle complex inference problems, and thus overcome the hurdle of complexity that can be present in décision prob-lems. Three studies-one on what to conclude when a database search provides exactly one hit, one on what genotype to search for in a database based on the observations made on DNA typing results, and one on whether to submit a fingermark to the process of comparing it with prints of its potential sources-explain the application of décision theory and influ¬ence diagrams to each of these décisions. The results of the theoretical case studies support the thesis's three propositions. Hence, this thesis présents a uniform framework for organizing and finding the most rational course of action in décision problems encountered by scientists in forensic science laboratories. The proposed framework is an interactive and exploratory tool for better understanding a décision problem so that this understanding may lead to better informed choices.

Population PK-guided simulation study in children exposed to drugs in human milk

Risks of significant infant drug exposure through human milk arepoorly defined due to lack of large-scale PK data. We propose to useBayesian approach based on population PK (popPK)-guided modelingand simulation for risk prediction. As a proof-of-principle study, weexploited fluoxetine milk concentration data from 25 women. popPKparameters including milk-to-plasma ratio (MP ratio) were estimatedfrom the best model. The dose of fluoxetine the breastfed infant wouldreceive through mother's milk, and infant plasma concentrations wereestimated from 1000 simulated mother-infant pairs, using randomassignment of feeding times and milk volume. A conservative estimateof CYP2D6 activity of 20% of the allometrically-adjusted adult valuewas assumed. Derived model parameters, including MP ratio were consistentwith those reported in the literature. Visual predictive check andother model diagnostics showed no signs of model misspecifications.The model simulation predicted that infant exposure levels to fluoxetinevia mother's milk were below 10% of weight-adjusted maternal therapeuticdoses in >99% of simulated infants. Predicted median ratio ofinfant-mother serum levels at steady state was 0.093 (range 0.033-0.31),consistent with literature reported values (mean=0.07; range 0-0.59).Predicted incidence of relatively high infant-mother ratio (>0.2) ofsteady-state serum fluoxetine concentrations was <1.3%. Overall, ourpredictions are consistent with clinical observations. Our approach maybe valid for other drugs, allowing in silico prediction of infant drugexposure risks through human milk. We will discuss application of thisapproach to another drug used in lactating women.

Secession and liberal democracy. The case of the Basque country

The academic debate about the secession of a territory which is part of a liberal democracy state displays an initial contrast. On the one hand, practical secessionist movements usually legitimize their position using nationalist arguments linked to the principle of national self- determination. On the other hand, we find in academia few defenders of a normative principle of national self-determination. Philosophers, political scientists and jurists usually defend the status quo. And even when they do not defend it, most of them tend to leave the question of that question and secession unresolved or confused. Regarding this issue, liberal-democratic theories show a tendency to be “conservative” in relation to the political borders, regardless the historical and empirical processes of creation of current States. Probably, this feature is not far away to the fact that, since its beginning, political liberalism has not been a theory of the nation, but a theory of the state.

Wandel der Biodiversität in der Schweiz seit 1900: ist die Talsohle erreicht?

Die Biodiversität ist unsere Lebensgrundlage - ihr ökonomischer, ökologischer, sozialer und ästhetischer Wert kann nicht hoch genug eingeschätzt werden. Im Jahr 2003 beschlossen die Umweltminister Europas daher, den Verlust der Biodiversität bis ins Jahr 2010 zu stoppen. Haben wir dieses Ziel erreicht?Die vorliegende Studie des Forum Biodiversität Schweiz gibt fundierte Antworten auf diese Frage. Die umfassende Analyse zeigt auf Basis der besten verfügbaren Daten und differenziert für unterschiedliche Aspekte der biologischen Vielfalt, wie sich die Biodiversität in der Schweiz seit 1900 entwickelt hat. Die Resultate zeigen, dass weiterhin ein großer Handlungsbedarf besteht.

Selvitys Eduskunnan lisärakennuksen taidekilpailusta

The purpose of this thesis was to investigate how and why an art competition was arranged to select pieces for the parliamentary annexe building in Helsinki. There is an emphasis on the cultural production aspects of the research. For the purpose of comparison, the thesis also examines how art acquisition takes place in the cities of Helsinki, Salo and Vantaa, and how the so-called percentage principle has been used in these cities The research method involved thematic interviewing of four persons with central positions on the competition jury. Questions were also sent by e-mail to experts and other people with knowledge of the subject area. Although art competitions have been arranged in Finland for decades, very little relevant literature exists. In addition to the interviews, other relevant literature was also referred to, including parliamentary records. The crucial questions concerned why the art competition for the parliamentary annexe was arranged and whether, indeed, it is possible to compete artistically in this manner. The thesis also examined the relationship between art and architecture and how the best works were selected from the vast range of submissions. The answers were both honest and interesting. The thesis presents a step-by-step analysis of the competition's progress over two stages, and according to the specific rules for such competitions as laid out in Suomen Taiteilijaseura. Strict adherence to the rules of the competition created a number of problems, some of which are also studied. The primary reason for staging a competition was to be as democratic as possible, and eliminating any possibility of nominating a particular artist or artists to realise their own work within the annexe. The competition opened up the possibility to consider various artistic proposals, and no genres were ruled out in advance. This format ensured a good response and a total of 1719 proposals were received, of which six were eventually selected. One conclusion was that open competition may not be the best way to gather artistic proposals in such circumstances, but it is very democratic.

Hakunilan Kultsa/Urban II hanke : pohdintaa yhteisöteatterin merkityksestä alueelle

This thesis analyses what local community theatre activity means to an area and its residents, and whether this kind of activity is meaningful. The objective was to explore whether and how community art can help urban areas to move in the direction of sustainable development: whether art can be part of regional policy development work. Hakunilan Kultsa was founded in 2003. It is an Urban II, European Union project and part of the Community Iniative Programme 2001-2006, financed by the EU. Hakunilan Kultsa is also a co-operation between Vantaa city council's culture and youth services. The project encourages Hakunila residents of different ages to take part in versatile art and cultural intrests in the Hakunila youth centre. People have the opportunity to participate in theatre, expression, arts, dance, performing arts and writing groups. One of the main aims is to found a sustainable community theatre in the area. The thesis examines what effects Hakunilan Kultsa has had so far. Inquiry form and thematical interviews have been used as research methods. Interviews and questionnaires were gathered between Autumn 2004 and Spring 2005. The whole process lasted from Spring 2004 until Spring 2006. The author also made participatory observations during the research process which in turn affected the conclusions. The thesis also deals with associated topics such as urban programmes, sustainable development, Hakunila as a suburban area, resident stimulation, and community thetare work. Hakunilan Kultsa has proved its importance. Based on the enquiries and interviews, the project has effectively presented the possibility for art forms to become hobbies. There is no cultural, age or economical discrimination. The easily accessible site and the low threshold principle make it easy for people to participate. The community theatre has improved the area's public image, increased participation and initiative, and given a voice to the community.

Relay card for capacitance measurements

In this bachelor's thesis a relay card for capacitance measurements was designed, built and tested. The study was made for the research and development laboratory of VTI Technologies, which manufactures capacitive silicon micro electro mechanical accelerometers and pressure sensors. As the size of the sensors is decreasing the capacitance value of the sensors also decreases. The decreased capacitance causes a need for new and more accurate measurement systems. The technology used in the instrument measuring the capacitance dictates a framework how the relay card should be designed, thus the operating principle of the instrument must be known. To achieve accurate results the measurement instrument and its functions needed to be used correctly. The relay card was designed using printed circuit board design methods that minimize interference coupling to the measurement. The relay card that was designed in this study is modular. It consists of a separate CPU card, which was used to control the add-on cards connected to it. The CPU card was controlled from a computer through a serial bus. Two add-on cards for the CPU card were designed in this study. The first one was the measurement card, which could be used to measure 32 capacitive sensors. The second add-on card was the MUX card, which could be used to switch between two measurement cards. The capacitance measurements carried out through the MUX card and the measurement cards were characterized with a series of test measurements. The test measurement data was then analysed. The relay card design was confirmed to work and offer accurate measurement results up to a measurement frequency of 10 MHz. The length of the measurement cables limited the measurement frequency.

ILS-ESP An efficient, simple, and parameter-free algorithm for solving the permutation flow-shop problem

From a managerial point of view, the more effcient, simple, and parameter-free (ESP) an algorithm is, the more likely it will be used in practice for solving real-life problems. Following this principle, an ESP algorithm for solving the Permutation Flowshop Sequencing Problem (PFSP) is proposed in this article. Using an Iterated Local Search (ILS) framework, the so-called ILS-ESP algorithm is able to compete in performance with other well-known ILS-based approaches, which are considered among the most effcient algorithms for the PFSP. However, while other similar approaches still employ several parameters that can affect their performance if not properly chosen, our algorithm does not require any particular fine-tuning process since it uses basic "common sense" rules for the local search, perturbation, and acceptance criterion stages of the ILS metaheuristic. Our approach defines a new operator for the ILS perturbation process, a new acceptance criterion based on extremely simple and transparent rules, and a biased randomization process of the initial solution to randomly generate different alternative initial solutions of similar quality -which is attained by applying a biased randomization to a classical PFSP heuristic. This diversification of the initial solution aims at avoiding poorly designed starting points and, thus, allows the methodology to take advantage of current trends in parallel and distributed computing. A set of extensive tests, based on literature benchmarks, has been carried out in order to validate our algorithm and compare it against other approaches. These tests show that our parameter-free algorithm is able to compete with state-of-the-art metaheuristics for the PFSP. Also, the experiments show that, when using parallel computing, it is possible to improve the top ILS-based metaheuristic by just incorporating to it our biased randomization process with a high-quality pseudo-random number generator.

Epigenetics in sepsis: targeting histone deacetylases.

Severe sepsis and septic shock are lethal complications of infection, characterised by dysregulated inflammatory and immune responses. Our understanding of the pathogenesis of sepsis has improved markedly in recent years, but unfortunately has not been translated into efficient treatment strategies. Epigenetic mechanisms such as covalent modification of histones by acetylation are master regulators of gene expression under physiological and pathological conditions, and strongly impact on inflammatory and host defence responses. Histone acetylation is controlled by histone acetyltransferases and histone deacetylases (HDACs), which affect gene expression also by targeting non-histone transcriptional regulators. Numerous HDAC inhibitors (HDACi) are being tested in clinical trials, primarily for the treatment of cancer. We performed the first comprehensive study of the impact of HDACi on innate immune responses in vitro and in vivo. We showed that HDACi act essentially as negative regulators of the expression of critical immune receptors and antimicrobial pathways in innate immune cells. In agreement, HDACi impaired phagocytosis and killing of bacteria by macrophages, and increased susceptibility to non-severe bacterial and fungal infections. Strikingly, proof-of-principle studies demonstrated that HDACi protect from lethal toxic shock and septic shock. Overall, our observations argue for a close monitoring of the immunological and infection status of patients treated with HDACi, especially immunocompromised cancer patients. They also support the concept of pharmacological inhibitors of HDACs as promising drugs to treat inflammatory diseases, including sepsis.

Performance assessment and league tables. Comparing like with like.

We formulate performance assessment as a problem of causal analysis and outline an approach based on the missing data principle for its solution. It is particularly relevant in the context of so-called league tables for educational, health-care and other public-service institutions. The proposed solution avoids comparisons of institutions that have substantially different clientele (intake).

Financial Development, Financial Fragility, and Growth

This paper studies the apparent contradiction between two strands of the literature on the effects of financial intermediation on economic activity. On the one hand, the empirical growth literature finds a positive effect of financial depth as measured by, for instance, private domestic credit and liquid liabilities (e.g., Levine, Loayza, and Beck 2000). On the other hand, the banking and currency crisis literature finds that monetary aggregates, such as domestic credit, are among the best predictors of crises and their related economic downturns (e.g., Kaminski and Reinhart 1999). The paper accounts for these contrasting effects based on the distinction between the short- and long-run impacts of financial intermediation. Working with a panel of cross-country and time-series observations, the paper estimates an encompassing model of short- and long-run effects using the Pooled Mean Group estimator developed by Pesaran, Shin, and Smith (1999). The conclusion from this analysis is that a positive long-run relationship between financial intermediation and output growth co-exists with a, mostly, negative short-run relationship. The paper further develops an explanation for these contrasting effects by relating them to recent theoretical models, by linking the estimated short-run effects to measures of financial fragility (namely, banking crises and financial volatility), and by jointly analyzing the effects of financial depth and fragility in classic panel growth regressions.

The pattern of health care use of older prisoners in Switzerland.

Introduction: Population ageing is a worldwide phenomenon that forces us to make radical changes on multiple levels of society. So far, studies have concluded that the health, both physical and mental, of prisoners in general and older prisoners in particular is worse than that of the general population. Prisoners are reported to age faster as compared to adults in the community. However, to date, very little is known about the actual healthcare conditions of older prisoners and almost no substantial knowledge is available concerning their patterns of healthcare use. Method: A quantitative study was conducted in four prisons for male prisoners in Switzerland, including two open and two closed prisons situated in different cantons. In this study, medical records of older prisoners (50+) were obtained from the respective authority upon consent and total anonymity was ensured. Data gathered from all available medical records included basic demographic information, education and prison sentencing. Healthcare data obtained were extensive in nature encompassing data related to illness types, number of visits to different health care providers and hospitals. The corresponding reasons for visits and outcomes of these visits were extracted. All data are analysed using statistical software SPSS 20.0. Results: Data were extracted for a total of 50 older prisoners living in Switzerland. The chosen prisons are located in German-speaking cantons. Preliminary results show that the age average was 56 years. For more than half, this was their first imprisonment. Nevertheless, a third of them were sentenced to measures (Art. 64 Swiss Criminal Code) which means that the length of the detention is indefinite and while release is possible it is in most cases not very likely. This entails that these prisoners will grow old in prison and some will even spend their remaining years there. Concerning their health, a third of the sample reported respiratory and cardiovascular illnesses and half reported suffering from some form of musculoskeletal related pain. Older prisoners were prescribed on average only 3.5 medications, which is significantly fewer than the number of medication prescribed to younger prisoners, whose data were also sampled. Conclusion: Access to healthcare is a right given to all prisoners through the principle of equivalence which is generally exercised in Switzerland. Prisoners growing old in prison will represent a challenge for prison health care services.