Organisational reforms in active welfare states: A comparative analysis of the turn to 'single gateways' in Western Europe

Based on the case of reforms aimed at integrating the provision of income protection and employment services for jobless people in Europe, this thesis seeks to understand the reasons which may prompt governments to engage in large-scale organisational reforms. Over the last 20 years, several European countries have indeed radically redesigned the organisational structure of their welfare state by merging or bundling existing front-line offices in charge of benefit payment and employment services together into 'one-stop' agencies. Whereas in academic and political debates, these reforms are generally presented as a necessary and rational response to the problems and inconsistencies induced by fragmentation in a context of the reorientation of welfare states towards labour market activation, this thesis shows that the agenda setting of these reforms is in fact the result of multidimensional political dynamics. More specifically, the main argument of this thesis is that these reforms are best understood not so such from the problems induced by organisational compartmentalism, whose political recognition is often controversial, but from the various goals that governments may simultaneously achieve by means of their adoption. This argument is tested by comparing agenda-setting processes of large-scale reforms of coordination in the United Kingdom (Jobcentre Plus), Germany (Hartz IV reform) and Denmark (2005 Jobcentre reform), and contrasting them with the Swiss case where the government has so far rejected any coordination initiative involving organisational redesign. This comparison brings to light the importance, for the rise of organisational reforms, of the possibility to couple them with the following three goals: first, goals related to the strengthening of activation policies; second, institutional goals seeking to redefine the balance of responsibilities between the central state and non-state actors, and finally electoral goals for governments eager to maintain political credibility. The decisive role of electoral goals in the three countries suggests that these reforms are less bound by partisan politics than by the particular pressures facing governments arrived in office after long periods in opposition.

Analysis of gene expression patterns in animals

During my PhD, my aim was to provide new tools to increase our capacity to analyse gene expression patterns, and to study on a large-scale basis the evolution of gene expression in animals. Gene expression patterns (when and where a gene is expressed) are a key feature in understanding gene function, notably in development. It appears clear now that the evolution of developmental processes and of phenotypes is shaped both by evolution at the coding sequence level, and at the gene expression level.Studying gene expression evolution in animals, with complex expression patterns over tissues and developmental time, is still challenging. No tools are available to routinely compare expression patterns between different species, with precision, and on a large-scale basis. Studies on gene expression evolution are therefore performed only on small genes datasets, or using imprecise descriptions of expression patterns.The aim of my PhD was thus to develop and use novel bioinformatics resources, to study the evolution of gene expression. To this end, I developed the database Bgee (Base for Gene Expression Evolution). The approach of Bgee is to transform heterogeneous expression data (ESTs, microarrays, and in-situ hybridizations) into present/absent calls, and to annotate them to standard representations of anatomy and development of different species (anatomical ontologies). An extensive mapping between anatomies of species is then developed based on hypothesis of homology. These precise annotations to anatomies, and this extensive mapping between species, are the major assets of Bgee, and have required the involvement of many co-workers over the years. My main personal contribution is the development and the management of both the Bgee database and the web-application.Bgee is now on its ninth release, and includes an important gene expression dataset for 5 species (human, mouse, drosophila, zebrafish, Xenopus), with the most data from mouse, human and zebrafish. Using these three species, I have conducted an analysis of gene expression evolution after duplication in vertebrates.Gene duplication is thought to be a major source of novelty in evolution, and to participate to speciation. It has been suggested that the evolution of gene expression patterns might participate in the retention of duplicate genes. I performed a large-scale comparison of expression patterns of hundreds of duplicated genes to their singleton ortholog in an outgroup, including both small and large-scale duplicates, in three vertebrate species (human, mouse and zebrafish), and using highly accurate descriptions of expression patterns. My results showed unexpectedly high rates of de novo acquisition of expression domains after duplication (neofunctionalization), at least as high or higher than rates of partitioning of expression domains (subfunctionalization). I found differences in the evolution of expression of small- and large-scale duplicates, with small-scale duplicates more prone to neofunctionalization. Duplicates with neofunctionalization seemed to evolve under more relaxed selective pressure on the coding sequence. Finally, even with abundant and precise expression data, the majority fate I recovered was neither neo- nor subfunctionalization of expression domains, suggesting a major role for other mechanisms in duplicate gene retention.

Qualitative and quantitative analysis of thalamo-cortical axons in the somatosensory cortex of normal and barrelless mice

Résumé Les rongeurs utilisent leurs moustaches (vibrisses) pour explorer le milieu environnant. Chaque moustache est mue par un système des muscles. Les récepteurs situés à sa base transmettent les informations au système nerveux central. La transmission vers l'écorce se fait via trois neurones de relais qui se trouvent au niveau du ganglion trigéminé, du tronc cérébral et du thalamus. La représentation corticale d'une vibrisse est une concentration des axones thalamo-corticaux (ATC) autour desquelles s'organisent leurs cibles, les cellules de la couche IV. La structure peut être identifiée histologiquement en coupes tangentielles et porte le nom de « barrel » (« tonneau »). Cette correspondance vibrisse - barrel fait de ce système un model idéal pour étudier l'influence de l'activité périphérique sur l'établissement et le maintien des cartes somatotopiques. Notre laboratoire dispose d'une souche de souris qui a subi une mutation spontanée pour le gène codant l'adenylyl cyclase I (ACI). Cette enzyme membranaire catalyse la formation de l'AMPc et joue un rôle important dans le guidage axonal, la libération des neurotransmetteurs et l'intégration des signaux postsynaptiques. Nous avons démontré dans un premier temps que cette souris adulte ne développe pas de barrels. Cela est dû à un manque d'organisation des ATC et aussi des cellules de la couche IV. De plus, les résultats électrophysiologiques montrent que les informations venant des vibrisses adjacentes ne sont pas intégrées d'une manière normale. Dans ce travail de thèse, j'ai analysé la morphologie des ATC révélés individuellement avec de la biocytine. L'analyse quantitative des ATC a mis en évidence les points suivants: 1. Les axones de la souris normale (NOR) quittent le thalamus, traversent la capsule interne et la substance blanche sous-corticale et pénètrent dans le cortex somato-sensoriel primaire. A l'intérieur de l'écorce ils traversent au maximum 3 colonnes corticales adjacentes dont une contient le barrel cible. En passant à travers les couches VI et V, ces axones arborisent et convergent progressivement vers le barrel dans lequel ils forment une riche arborisation. Un petit nombre des branches « errantes », pleines de boutons synaptiques, pénètrent dans les barrels voisins. Deux axones NOR provenant de corps cellulaires très proches dans le thalamus peuvent avoir un cheminement très divergent lors de la traversée de la capsule interne et de la substance blanche sous-corticale mais, à leur entrée dans le cortex, ils sont distants d'au maximum 2 colonnes corticales de la colonne qui contient le barrel cible et ils convergent progressivement vers ce barrel. 2. Les axones de la souris mutante (BRL) ont le même trajet sous-cortical que les axones NOR, mais leur entrée dans le cortex somato-sensoriel primaire est aléatoire. A l'interface entre la substance blanche sous-corticale et le cortex, l'axone principal se divise rapidement en troncs axonaux qui traversent les couches VI et V d'une manière divergente pour arriver dans la couche IV. Cela contraste beaucoup avec la trajectoire des NOR qui convergent graduellement vers leur barrel cible. Le nombre de branches radiales que les axones BRL utilisent pour entrer dans le cortex et dans la couche IV est double par rapport aux axones NOR. Parmi ces branches, seules quelques-unes donnent des arborisations, les autres ne sont pas développées et leur morphologie est semblable à celle des branches formées par les axones de la souris normale lors du développement. Deux axones BRL issus de corps cellulaires proches dans le thalamus peuvent avoir une trajectoire très divergente jusqu'à leur entrée dans la couche IV, mais à ce niveau ils sont réorientés pour se retrouver et faire un nombre maximal de branches et boutons synaptiques dans la même région corticale. Dans un cas extrême, un des axones observés est entré dans le cortex à la limite entre l'aire somatosensorielle primaire et secondaire et a parcouru une distance de 2 mm pour retrouver son partenaire thalamique et donner avec celui-ci un nombre maximal de branches dans la même région de la couche IV. 3. Les mesures quantitatives ont montré que les arborisations corticales des axones NOR ont une longueur moyenne de 18mm et sont formées par 200 segments qui portent 1200 boutons synaptiques. Par rapport à la souris NOR, les axones BRL ont en moyenne la même longueur, le même nombre de segments et boutons synaptiques, mais donnent deux fois plus de branches radiales. La surface tangentielle occupée par les arborisations BRL dans la couche IV est 2 fois plus grande que celle des NOR. Cela signifie que les 1000 boutons synaptiques qui caractérisent les arborisations NOR et BRL dans la couche IV sont disséminés sur une surface tangentielle double chez les derniers, et donc que la densité des boutons par unité de surface corticale est en moyenne plus faible. En effet, l'augmentation de la surface corticale tangentielle des BRL est due aux surfaces de faible et moyenne densité synaptique (0 - 8 boutons / 400pn2) qui augmentent 2 fois tandis que les surfaces de haute densité synaptiques (8 - 64 boutons / 4001.tm2) sont les mêmes. Nous émettons l'hypothèse selon laquelle, durant le développement, les ATC de la souris BRL divergent et forment un nombre exubérant de branches. Grâce à cette divergence et aux branches supranuméraires, ils trouvent l'endroit de l'écorce où se trouvent leurs voisins thalamiques et arborisent abondamment dans cette région. Cependant, le déficit en AGI ne leurs permet pas par la suite, sous influence de l'activité périphérique, de retirer les branches qui se trouvent dans les endroits inappropriés de l'écorce, avec de possibles conséquences sur la discrimination tactile.

Analysis of naturally acquired CD4+T-cell responses to MAGE-A3 and MAGE-A4 cancer/testis antigens in patients with resected head and neck squamous cell carcinoma

Despite advances in the medical and surgical treatment of Head and Neck (HN) squamous cell carcinoma (HNSCC), long term survival has remained unchanged in the last 20 years. The obvious limitations of traditional therapeutic options strongly urge the development of novel therapeutic approaches. The molecular cloning of tumor antigens recognized by T lymphocytes in recent years has provided targets for specific immunotherapy. In this regard, frequent expression of Cancer Testis Antigens (CTA) has been repeatedly observed among HN tumors. We analyzed CTA expression in 46 HNSCC patients and found that MAGE-A3 and/or -A4 CTA were positive in over 70% of samples, regardless of the anatomical site of primary tumors in the upper aerodigestive tract. Still, immune responses against these CTA in HNSCC patients have not yet been investigated in detail. In this study we assessed the responsiveness of HNSCC patient's lymphocytes against overlapping peptides spanning the entire MAGE-A3 and -A4 proteins. After depletion of CD4+CD25+ regulatory T cells, and following three rounds of in vitro stimulation with pools of overlapping peptides, peripheral blood mononuclear cells (PBMCs) of HNSCC patients were screened by IFN-g and TNF-a intracellular cytokine staining for reactivity against MAGE-A3 or -A4 derived peptides. Cytokine secreting CD4+ T cells, specific for several peptides, were detected in 7/7 patients. In contrast, only 2/5 PBMC from healthy donors showed weak T cell responses against 2 peptides. CD4+ T cells specific for one epitope MAGE-A3(281-295), previously described as an HLA-DR11 restricted epitope naturally processed and presented by dendritic cells and tumor cells, were detected in two patients. MAGE-A3(161-175) specific CD4+ T cells were found in one patient. Six MAGE-A3 and -A4 new epitopes are being characterized. Together, these data suggest that naturally acquired CD4+ T cell responses against CT antigens occur in vivo in HNSCC patients, providing a rational basis for the use of the identified peptides in vaccination protocols.

Detecting and measuring deprivation in primary care: development, validity and reliability of a self-reported questionnaire - the DiPCare-Q

Background: General practitioners play a central role in taking deprivation into consideration when caring for patients in primary care. Validated questions to identify deprivation in primary-care practices are still lacking. For both clinical and research purposes, this study therefore aims to develop and validate a standardized instrument measuring both material and social deprivation at an individual level. Methods: The Deprivation in Primary Care Questionnaire (DiPCare-Q) was developed using qualitative and quantitative approaches between 2008 and 2011. A systematic review identified 199 questions related to deprivation. Using judgmental item quality, these were reduced to 38 questions. Two focus groups (primary-care physicians, and primary-care researchers), structured interviews (10 laymen), and think aloud interviews (eight cleaning staff) assured face validity. Item response theory analysis was then used to derive the DiPCare-Q index using data obtained from a random sample of 200 patients who were to complete the questionnaire a second time over the phone. For construct and criterion validity, the final 16 questions were administered to a random sample of 1,898 patients attending one of 47 different private primary-care practices in western Switzerland (validation set) along with questions on subjective social status (subjective SES ladder), education, source of income, welfare status, and subjective poverty. Results: Deprivation was defined in three distinct dimensions (table); material deprivation (eight items), social deprivation (five items) and health deprivation (three items). Item consistency was high in both the derivation (KR20 = 0.827) and the validation set (KR20 = 0.778). The DiPCare-Q index was reliable (ICC = 0.847). For construct validity, we showed the DiPCare-Q index to be correlated to patients' estimation of their position on the subjective SES ladder (rs = 0.539). This position was correlated to both material and social deprivation independently suggesting two separate mechanisms enhancing the feeling of deprivation. Conclusion: The DiPCare-Q is a rapid, reliable and validated instrument useful for measuring both material and social deprivation in primary care. Questions from the DiPCare-Q are easy to use when investigating patients' social history and could improve clinicians' ability to detect underlying social distress related to deprivation.

Evolutionary history of the greater white-toothed shrew (Crocidura russula) inferred from analysis of mtDNA, Y, and X chromosome markers.

We investigate the evolutionary history of the greater white-toothed shrew across its distribution in northern Africa and mainland Europe using sex-specific (mtDNA and Y chromosome) and biparental (X chromosome) markers. All three loci confirm a large divergence between eastern (Tunisia and Sardinia) and western (Morocco and mainland Europe) lineages, and application of a molecular clock to mtDNA divergence estimates indicates a more ancient separation (2.25 M yr ago) than described by some previous studies, supporting claims for taxonomic revision. Moroccan ancestry for the mainland European population is inconclusive from phylogenetic trees, but is supported by greater nucleotide diversity and a more ancient population expansion in Morocco than in Europe. Signatures of rapid population expansion in mtDNA, combined with low X and Y chromosome diversity, suggest a single colonization of mainland Europe by a small number of Moroccan shrews >38 K yr ago. This study illustrates that multilocus genetic analyses can facilitate the interpretation of species' evolutionary history but that phylogeographic inference using X and Y chromosomes is restricted by low levels of observed polymorphism.

A critical analysis of three psychological research programs of doping behaviour

Objectives To consider the various specific substances-taking activities in sport an examination of three psychological models of doping behaviour utilised by researchers is presented in order to evaluate their real and potential impact, and to improve the relevance and efficiency of anti-doping campaigns. Design Adopting the notion of a "research program" (Lakatos, 1978) from the philosophy of science, a range of studies into the psychology of doping behaviour are classified and critically analysed. Method Theoretical and practical parameters of three research programs are critically evaluated (i) cognitive; (ii) drive; and (iii) situated-dynamic. Results The analysis reveals the diversity of theoretical commitments of the research programs and their practical consequences. The «cognitive program» assumes that athletes are accountable for their acts that reflect the endeavour to attain sporting and non-sporting goals. Attitudes, knowledge and rational decisions are understood to be the basis of doping behaviour. The «drive program» characterises the variety of traces and consequences on psychological and somatic states coming from athlete's experience with sport. Doping behaviour here is conceived of as a solution to reduce unconscious psychological and somatic distress. The «situated-dynamic program» considers a broader context of athletes' doping activity and its evolution during a sport career. Doping is considered as emergent and self-organized behaviour, grounded on temporally critical couplings between athletes' actions and situations and the specific dynamics of their development during the sporting life course. Conclusions These hypothetical, theoretical and methodological considerations offer a more nuanced understanding of doping behaviours, making an effective contribution to anti-doping education and research by enabling researchers and policy personnel to become more critically reflective about their explicit and implicit assumptions regarding models of explanations for doping behaviour.

A system-level, molecular evolutionary analysis of mammalian phototransduction

Visual perception is initiated in the photoreceptor cells of the retina via the phototransduction system.This system has shown marked evolution during mammalian divergence in such complex attributes as activation time and recovery time. We have performed a molecular evolutionary analysis of proteins involved in mammalianphototransduction in order to unravel how the action of natural selection has been distributed throughout thesystem to evolve such traits. We found selective pressures to be non-randomly distributed according to both a simple protein classification scheme and a protein-interaction network representation of the signaling pathway. Proteins which are topologically central in the signaling pathway, such as the G proteins, as well as retinoid cycle chaperones and proteins involved in photoreceptor cell-type determination, were found to be more constrained in their evolution. Proteins peripheral to the pathway, such as ion channels and exchangers, as well as the retinoid cycle enzymes, have experienced a relaxation of selective pressures. Furthermore, signals of positive selection were detected in two genes: the short-wave (blue) opsin (OPN1SW) in hominids and the rod-specific Na+/Ca2+,K+ ion exchanger (SLC24A1) in rodents. The functions of the proteins involved in phototransduction and the topology of the interactions between them have imposed non-random constraints on their evolution. Thus, in shaping or conserving system-level phototransduction traits, natural selection has targeted the underlying proteins in a concerted manner.

Evolutionary analysis of genetic variants involved in rare diseases

Next-generation sequencing techniques such as exome sequencing can successfully detect all genetic variants in a human exome and it has been useful together with the implementation of variant filters to identify causing-disease mutations. Two filters aremainly used for the mutations identification: low allele frequency and the computational annotation of the genetic variant. Bioinformatic tools to predict the effect of a givenvariant may have errors due to the existing bias in databases and sometimes show a limited coincidence among them. Advances in functional and comparative genomics are needed in order to properly annotate these variants.The goal of this study is to: first, functionally annotate Common Variable Immunodeficiency disease (CVID) variants with the available bioinformatic methods in order to assess the reliability of these strategies. Sencondly, as the development of new methods to reduce the number of candidate genetic variants is an active and necessary field of research, we are exploring the utility of gene function information at organism level as a filter for rare disease genes identification. Recently, it has been proposed that only 10-15% of human genes are essential and therefore we would expect that severe rare diseases are mostly caused by mutations on them. Our goal is to determine whether or not these rare and severe diseases are caused by deleterious mutations in these essential genes. If this hypothesis were true, taking into account essential genes as a filter would be an interesting parameter to identify causingdisease mutations.

Simulation and Analysis of Arterial Traffic Operations Along the U.S. 61 Corridor in Burlington, Iowa, 1998

The Center for Transportation Research and Education (CTRE) used the traffic simulation model CORSIM to access proposed capacity and safety improvement strategies for the U.S. 61 corridor through Burlington, Iowa. The comparison between the base and alternative models allow for evaluation of the traffic flow performance under the existing conditions as well as other design scenarios. The models also provide visualization of performance for interpretation by technical staff, public policy makers, and the public. The objectives of this project are to evaluate the use of traffic simulation models for future use by the Iowa Department of Transportation (DOT) and to develop procedures for employing simulation modeling to conduct the analysis of alternative designs. This report presents both the findings of the U.S. 61 evaluation and an overview of model development procedures. The first part of the report includes the simulation modeling development procedures. The simulation analysis is illustrated through the Burlington U.S. 61 corridor case study application. Part I is not intended to be a user manual but simply introductory guidelines for traffic simulation modeling. Part II of the report evaluates the proposed improvement concepts in a side by side comparison of the base and alternative models.

Density, climate and varying return points: an analysis of long-term population fluctuations in the threatened European tree frog.

Experimental research has identified many putative agents of amphibian decline, yet the population-level consequences of these agents remain unknown, owing to lack of information on compensatory density dependence in natural populations. Here, we investigate the relative importance of intrinsic (density-dependent) and extrinsic (climatic) factors impacting the dynamics of a tree frog (Hyla arborea) population over 22 years. A combination of log-linear density dependence and rainfall (with a 2-year time lag corresponding to development time) explain 75% of the variance in the rate of increase. Such fluctuations around a variable return point might be responsible for the seemingly erratic demography and disequilibrium dynamics of many amphibian populations.

Association between the PNPLA3 (rs738409 C>G) variant and hepatocellular carcinoma: Evidence from a meta-analysis of individual participant data.

The incidence of hepatocellular carcinoma (HCC) is increasing in Western countries. Although several clinical factors have been identified, many individuals never develop HCC, suggesting a genetic susceptibility. However, to date, only a few single-nucleotide polymorphisms have been reproducibly shown to be linked to HCC onset. A variant (rs738409 C>G, encoding for p.I148M) in the PNPLA3 gene is associated with liver damage in chronic liver diseases. Interestingly, several studies have reported that the minor rs738409[G] allele is more represented in HCC cases in chronic hepatitis C (CHC) and alcoholic liver disease (ALD). However, a significant association with HCC related to CHC has not been consistently observed, and the strength of the association between rs738409 and HCC remains unclear. We performed a meta-analysis of individual participant data including 2,503 European patients with cirrhosis to assess the association between rs738409 and HCC, particularly in ALD and CHC. We found that rs738409 was strongly associated with overall HCC (odds ratio [OR] per G allele, additive model=1.77; 95% confidence interval [CI]: 1.42-2.19; P=2.78 × 10(-7) ). This association was more pronounced in ALD (OR=2.20; 95% CI: 1.80-2.67; P=4.71 × 10(-15) ) than in CHC patients (OR=1.55; 95% CI: 1.03-2.34; P=3.52 × 10(-2) ). After adjustment for age, sex, and body mass index, the variant remained strongly associated with HCC. Conclusion: Overall, these results suggest that rs738409 exerts a marked influence on hepatocarcinogenesis in patients with cirrhosis of European descent and provide a strong argument for performing further mechanistic studies to better understand the role of PNPLA3 in HCC development.

Safety Analysis of Low-Volume Rural Roads in Iowa, 2010

Iowa features an extensive surface transportation system, with more than 110,000 miles of roadway, most of which is under the jurisdiction of local agencies. Given that Iowa is a lower-population state, most of this mileage is located in rural areas that exhibit low traffic volumes of less than 400 vehicles per day. However, these low-volume rural roads also account for about half of all recorded traffic crashes in Iowa, including a high percentage of fatal and major injury crashes. This study was undertaken to examine these crashes, identify major contributing causes, and develop low-cost strategies for reducing the incidence of these crashes. Iowa’s extensive crash and roadway system databases were utilized to obtain needed data. Using descriptive statistics, a test of proportions, and crash modeling, various classes of rural secondary roads were compared to similar state of Iowa controlled roads in crash frequency, severity, density, and rate for numerous selected factors that could contribute to crashes. The results of this study allowed the drawing of conclusions as to common contributing factors for crashes on low-volume rural roads, both paved and unpaved. Due to identified higher crash statistics, particular interest was drawn to unpaved rural roads with traffic volumes greater than 100 vehicles per day. Recommendations for addressing these crashes with low-cost mitigation are also included. Because of the isolated nature of traffic crashes on low-volume roads, a systemic or mass action approach to safety mitigation was recommended for an identified subset of the entire system. In addition, future development of a reliable crash prediction model is described.

Phenotypic and functional analysis of human fetal liver hematopoietic stem cells in culture.

Steady-state hematopoiesis and hematopoietic transplantation rely on the unique potential of stem cells to undergo both self-renewal and multilineage differentiation. Fetal liver (FL) represents a promising alternative source of hematopoietic stem cells (HSCs), but limited by the total cell number obtained in a typical harvest. We reported that human FL nonobese diabetic/severe combined immunodeficient (NOD/SCID) repopulating cells (SRCs) could be expanded under simple stroma-free culture conditions. Here, we sought to further characterize FL HSC/SRCs phenotypically and functionally before and following culture. Unexpanded or cultured FL cell suspensions were separated into various subpopulations. These were tested for long-term culture potential and for in vivo repopulating function following transplantation into NOD/SCID mice. We found that upon culture of human FL cells, a tight association between classical stem cell phenotypes, such as CD34(+) /CD38(-) and/or side population, and NOD/SCID repopulating function was lost, as observed with other sources. Although SRC activity before and following culture consistently correlated with the presence of a CD34(+) cell population, we provide evidence that, contrary to umbilical cord blood and adult sources, stem cells present in both CD34(+) and CD34(-) FL populations can sustain long-term hematopoietic cultures. Furthermore, upon additional culture, CD34-depleted cell suspensions, devoid of SRCs, regenerated a population of CD34(+) cells possessing SRC function. Our studies suggest that compared to neonatal and adult sources, the phenotypical characteristics of putative human FL HSCs may be less strictly defined, and reinforce the accumulated evidence that human FL represents a unique, valuable alternative and highly proliferative source of HSCs for clinical applications.