The emergence of parental and paternity leaves in Switzerland : a challenge to gendered representations and practices of parenthood?

The thesis addresses the issue of parenthood and gender equality in Switzerland through the emergence of parental leave policies. This is an original and relevant research topic, as Switzerland is one of the few industrialized countries that have not yet implemented a parental or paternity leave. I first describe the emergence of parental leave policies in the last ten to fifteen years in the political, media, and labor-market spheres. Secondly, adopting a gender and discursive theoretical approach, I analyze whether and to what extent this emergence challenged gendered representations and practices of parenthood. The multilevel and mixed-methods research design implies analyzing various data sets such as parliamentary interventions (N=23J and newspaper articles (N=579) on parental leave policies. A case study of a public administration which implemented a one-month paid paternity leave draws on register data of leave recipients (N=95) and in-depth interviews with fathers and managers (n=30). Results show that parental leave policies, especially in recent years, have been increasingly problematized in the three social spheres considered, as a result of political and institutional events. While there is a struggle over the definition of the legitimate leave type to implement [parental or paternity leave) in the political sphere, paternity leave has precedence in the media and labor-market spheres. Overall, this emergence contributes to making fatherhood visible in the public sphere, challenging albeit in a limited way gendered representations and practices of parenthood. Along with representations of involved fatherhood and change in gender relations, different roles and responsibilities are attributed to mothers and fathers, the latter being often defined as secondary, temporary and optional parents. Finally, I identify a common trend, namely the increasing importance of the economic aspects of parental leave policies with the consequence of sidelining their gender-equality potential. The dissertation contributes to the literature which analyzes the interconnections between the macro-, the meso- and the micro-levels of society in the constitution of gender relations and parenthood. It also provides useful tools for the analysis of the politics of parental leave policies in Switzerland and their effects for gender equality. - Cette thèse traite de la parentalité et de l'égalité de genre en Suisse à travers l'émergence des congés parentaux. Ce sujet de recherche est original et pertinent puisque la Suisse est à ce jour un des seuls pays industrialisés à ne pas avoir adopté de droit au congé parental ou paternité. Cette recherche décrit l'émergence des congés parentaux au cours des 10 à 15 dernières années dans les sphères politique, médiatique et du marché de l'emploi en Suisse. En combinant perspective de genre et analyse de discours, elle examine dans quelle mesure cette émergence remet en question les représentations et pratiques genrées de parentalité. Des méthodes de recherche mixtes sont employées pour analyser des interventions parlementaires (N=23) et des articles de presse (N=579) sur les congés parentaux. L'étude de cas d une entreprise publique qui a adopté un congé paternité payé d'un mois s'appuie sur des données de registre (N=95) et des entretiens semi-structurés avec des pères et des cadres (n=30). Les résultats indiquent que dans les trois sphères considérées, les congés parentaux ont reçu une attention croissante au cours de ces dernières années, en lien avec des événements politiques et institutionnels. Alors que dans la sphère politique il n'y a pas de consensus quant au type de congé considéré comme légitime (congé parental ou paternité), dans les sphères médiatique et du marché de l'emploi le congé paternité semble l'emporter. Dans l'ensemble, l'émergence des congés parentaux contribue à rendre la paternité plus visible dans l'espace public, remettant en question-bien que d'une manière limitée-les représentations genrées de la parentalité. En effet, d'une part l'image de pères impliqués et de rapports de genre plus égalitaires au sein de la famille est diffusée. D'autre part, mères et pères continuent à être associés à des rôles différents, les pères étant définis comme des parents secondaires et temporaires. Finalement, l'analyse révèle une tendance générale, soit l'importance croissante accordée aux aspects économiques des congés parentaux, avec pour conséquence la mise à l'écart de leur potentiel pour l'égalité de genre. Cette thèse contribue à la recherche sur les liens entre les niveaux macro- meso- et microsociaux dans la constitution des rapports de genre et de la parentalité. Elle propose également des outils pour analyser les politiques de congés parentaux en Suisse et leurs implications pour l'égalité de genre.

Reconciling phonological neighborhood effects in speech production through single trial analysis

A crucial step for understanding how lexical knowledge is represented is to describe the relative similarity of lexical items, and how it influences language processing. Previous studies of the effects of form similarity on word production have reported conflicting results, notably within and across languages. The aim of the present study was to clarify this empirical issue to provide specific constraints for theoretical models of language production. We investigated the role of phonological neighborhood density in a large-scale picture naming experiment using fine-grained statistical models. The results showed that increasing phonological neighborhood density has a detrimental effect on naming latencies, and re-analyses of independently obtained data sets provide supplementary evidence for this effect. Finally, we reviewed a large body of evidence concerning phonological neighborhood density effects in word production, and discussed the occurrence of facilitatory and inhibitory effects in accuracy measures. The overall pattern shows that phonological neighborhood generates two opposite forces, one facilitatory and one inhibitory. In cases where speech production is disrupted (e.g. certain aphasic symptoms), the facilitatory component may emerge, but inhibitory processes dominate in efficient naming by healthy speakers. These findings are difficult to accommodate in terms of monitoring processes, but can be explained within interactive activation accounts combining phonological facilitation and lexical competition.

Towards a dynamic model of e-commerce: environmental, technological and organisational drivers of B2C along time

Despite the important benefits for firms of commercial initiatives on the Internet, e-commerce is still an emerging distribution channel, even in developed countries. Thus, more needs to be known about the mechanisms affecting its development. A large number of works have studied firms¿ e-commerce adoption from technological, intraorganizational, institutional, or other specific perspectives, but there is a need for adequately tested integrative frameworks. Hence, this work proposes and tests a model of firms¿ business-to-consumer (called B2C) e-commerce adoption that is founded on a holistic vision of the phenomenon. With this integrative approach, the authors analyze the joint influence of environmental, technological, and organizational factors; moreover, they evaluate this effect over time. Using various representative Spanish data sets covering the period 1996-2005, the findings demonstrate the suitability of the holistic framework. Likewise, some lessons are learned from the analysis of the key building blocks. In particular, the current study provides evidence for the debate about the effect of competitive pressure, since the findings show that competitive pressure disincentivizes e-commerce adoption in the long term. The results also show that the development or enrichment of the consumers¿ consumption patterns, the technological readiness of the market forces, the firm¿s global scope, and its competences in innovation continuously favor e-commerce adoption.

Comparison of molecular signatures from multiple skin diseases identifies mechanisms of immunopathogenesis.

The ability to obtain gene expression profiles from human disease specimens provides an opportunity to identify relevant gene pathways, but is limited by the absence of data sets spanning a broad range of conditions. Here, we analyzed publicly available microarray data from 16 diverse skin conditions in order to gain insight into disease pathogenesis. Unsupervised hierarchical clustering separated samples by disease as well as common cellular and molecular pathways. Disease-specific signatures were leveraged to build a multi-disease classifier, which predicted the diagnosis of publicly and prospectively collected expression profiles with 93% accuracy. In one sample, the molecular classifier differed from the initial clinical diagnosis and correctly predicted the eventual diagnosis as the clinical presentation evolved. Finally, integration of IFN-regulated gene programs with the skin database revealed a significant inverse correlation between IFN-β and IFN-γ programs across all conditions. Our study provides an integrative approach to the study of gene signatures from multiple skin conditions, elucidating mechanisms of disease pathogenesis. In addition, these studies provide a framework for developing tools for personalized medicine toward the precise prediction, prevention, and treatment of disease on an individual level.

A stroma-related gene signature predicts resistance to neoadjuvant chemotherapy in breast cancer.

To better understand the relationship between tumor-host interactions and the efficacy of chemotherapy, we have developed an analytical approach to quantify several biological processes observed in gene expression data sets. We tested the approach on tumor biopsies from individuals with estrogen receptor-negative breast cancer treated with chemotherapy. We report that increased stromal gene expression predicts resistance to preoperative chemotherapy with 5-fluorouracil, epirubicin and cyclophosphamide (FEC) in subjects in the EORTC 10994/BIG 00-01 trial. The predictive value of the stromal signature was successfully validated in two independent cohorts of subjects who received chemotherapy but not in an untreated control group, indicating that the signature is predictive rather than prognostic. The genes in the signature are expressed in reactive stroma, according to reanalysis of data from microdissected breast tumor samples. These findings identify a previously undescribed resistance mechanism to FEC treatment and suggest that antistromal agents may offer new ways to overcome resistance to chemotherapy.

Comparative transcriptomics of early dipteran development

BACKGROUND: Modern sequencing technologies have massively increased the amount of data available for comparative genomics. Whole-transcriptome shotgun sequencing (RNA-seq) provides a powerful basis for comparative studies. In particular, this approach holds great promise for emerging model species in fields such as evolutionary developmental biology (evo-devo). RESULTS: We have sequenced early embryonic transcriptomes of two non-drosophilid dipteran species: the moth midge Clogmia albipunctata, and the scuttle fly Megaselia abdita. Our analysis includes a third, published, transcriptome for the hoverfly Episyrphus balteatus. These emerging models for comparative developmental studies close an important phylogenetic gap between Drosophila melanogaster and other insect model systems. In this paper, we provide a comparative analysis of early embryonic transcriptomes across species, and use our data for a phylogenomic re-evaluation of dipteran phylogenetic relationships. CONCLUSIONS: We show how comparative transcriptomics can be used to create useful resources for evo-devo, and to investigate phylogenetic relationships. Our results demonstrate that de novo assembly of short (Illumina) reads yields high-quality, high-coverage transcriptomic data sets. We use these data to investigate deep dipteran phylogenetic relationships. Our results, based on a concatenation of 160 orthologous genes, provide support for the traditional view of Clogmia being the sister group of Brachycera (Megaselia, Episyrphus, Drosophila), rather than that of Culicomorpha (which includes mosquitoes and blackflies).

Reexamination of the relationship of resting metabolic rate to fat-free mass and to the metabolically active components of fat-free mass in humans.

The ratio of resting metabolic rate (RMR) to fat-free mass (FFM) is often used to compare individuals of different body sizes. Because RMR has not been well described over the full range of FFM, a literature review was conducted among groups with a wide range of FFM. It included 31 data sets comprising a total of 1111 subjects: 118 infants and preschoolers, 323 adolescents, and 670 adults; FFM ranged from 2.8 to 106 kg. The relationship of RMR to FFM was found to be nonlinear and average slopes of the regression equations of the three groups differed significantly (P less than 0.0001). For only the youngest group did the intercept approach zero. The lower slopes of RMR on FFM, at higher measures of FFM, corresponded to relatively greater proportions of less metabolically active muscle mass and to lesser proportions of more metabolically active nonmuscle organ mass. Because the contribution of FFM to RMR is not constant, an arithmetic error is introduced when the ratio of RMR to FFM is used. Hence, alternative methods should be used to compare individuals with markedly different FFM.

Identification of a Poor-Prognosis BRAF-Mutant-Like Population of Patients With Colon Cancer.

PURPOSE Our purpose was development and assessment of a BRAF-mutant gene expression signature for colon cancer (CC) and the study of its prognostic implications. Materials and METHODS A set of 668 stage II and III CC samples from the PETACC-3 (Pan-European Trails in Alimentary Tract Cancers) clinical trial were used to assess differential gene expression between c.1799T>A (p.V600E) BRAF mutant and non-BRAF, non-KRAS mutant cancers (double wild type) and to construct a gene expression-based classifier for detecting BRAF mutant samples with high sensitivity. The classifier was validated in independent data sets, and survival rates were compared between classifier positive and negative tumors. Results A 64 gene-based classifier was developed with 96% sensitivity and 86% specificity for detecting BRAF mutant tumors in PETACC-3 and independent samples. A subpopulation of BRAF wild-type patients (30% of KRAS mutants, 13% of double wild type) showed a gene expression pattern and had poor overall survival and survival after relapse, similar to those observed in BRAF-mutant patients. Thus they form a distinct prognostic subgroup within their mutation class. CONCLUSION A characteristic pattern of gene expression is associated with and accurately predicts BRAF mutation status and, in addition, identifies a population of BRAF mutated-like KRAS mutants and double wild-type patients with similarly poor prognosis. This suggests a common biology between these tumors and provides a novel classification tool for cancers, adding prognostic and biologic information that is not captured by the mutation status alone. These results may guide therapeutic strategies for this patient segment and may help in population stratification for clinical trials.

PAX3/FOXO1 fusion gene status is the key prognostic molecular marker in rhabdomyosarcoma and significantly improves current risk stratification.

PURPOSE: To improve the risk stratification of patients with rhabdomyosarcoma (RMS) through the use of clinical and molecular biologic data. PATIENTS AND METHODS: Two independent data sets of gene-expression profiling for 124 and 101 patients with RMS were used to derive prognostic gene signatures by using a meta-analysis. These and a previously published metagene signature were evaluated by using cross validation analyses. A combined clinical and molecular risk-stratification scheme that incorporated the PAX3/FOXO1 fusion gene status was derived from 287 patients with RMS and evaluated. RESULTS: We showed that our prognostic gene-expression signature and the one previously published performed well with reproducible and significant effects. However, their effect was reduced when cross validated or tested in independent data and did not add new prognostic information over the fusion gene status, which is simpler to assay. Among nonmetastatic patients, patients who were PAX3/FOXO1 positive had a significantly poorer outcome compared with both alveolar-negative and PAX7/FOXO1-positive patients. Furthermore, a new clinicomolecular risk score that incorporated fusion gene status (negative and PAX3/FOXO1 and PAX7/FOXO1 positive), Intergroup Rhabdomyosarcoma Study TNM stage, and age showed a significant increase in performance over the current risk-stratification scheme. CONCLUSION: Gene signatures can improve current stratification of patients with RMS but will require complex assays to be developed and extensive validation before clinical application. A significant majority of their prognostic value was encapsulated by the fusion gene status. A continuous risk score derived from the combination of clinical parameters with the presence or absence of PAX3/FOXO1 represents a robust approach to improving current risk-adapted therapy for RMS.

A user-friendly web portal for T-Coffee on supercomputers

Background: Parallel T-Coffee (PTC) was the first parallel implementation of the T-Coffee multiple sequence alignment tool. It is based on MPI and RMA mechanisms. Its purpose is to reduce the execution time of the large-scale sequence alignments. It can be run on distributed memory clusters allowing users to align data sets consisting of hundreds of proteins within a reasonable time. However, most of the potential users of this tool are not familiar with the use of grids or supercomputers. Results: In this paper we show how PTC can be easily deployed and controlled on a super computer architecture using a web portal developed using Rapid. Rapid is a tool for efficiently generating standardized portlets for a wide range of applications and the approach described here is generic enough to be applied to other applications, or to deploy PTC on different HPC environments. Conclusions: The PTC portal allows users to upload a large number of sequences to be aligned by the parallel version of TC that cannot be aligned by a single machine due to memory and execution time constraints. The web portal provides a user-friendly solution.

Compliance with preoperative oral nutritional supplements in patients at nutritional risk─only a question of will?

BACKGROUND/OBJECTIVES: Preoperative nutrition has been shown to reduce morbidity after major gastrointestinal (GI) surgery in selected patients at risk. In a randomized trial performed recently (NCT00512213), almost half of the patients, however, did not consume the recommended dose of nutritional intervention. The present study aimed to identify the risk factors for noncompliance. SUBJECTS/METHODS: Demographic (n=5) and nutritional (n=21) parameters for this retrospective analysis were obtained from a prospectively maintained database. The outcome of interest was compliance with the allocated intervention (ingestion of ⩾11/15 preoperative oral nutritional supplement units). Uni- and multivariate analyses of potential risk factors for noncompliance were performed. RESULTS: The final analysis included 141 patients with complete data sets for the purpose of the study. Fifty-nine patients (42%) were considered noncompliant. Univariate analysis identified low C-reactive protein levels (P=0.015), decreased recent food intake (P=0.032) and, as a trend, low hemoglobin (P=0.065) and low pre-albumin (P=0.056) levels as risk factors for decreased compliance. However, none of them was retained as an independent risk factor after multivariate analysis. Interestingly, 17 potential explanatory parameters, such as upper GI cancer, weight loss, reduced appetite or co-morbidities, did not show any significant correlation with reduced intake of nutritional supplements. CONCLUSIONS: Reduced compliance with preoperative nutritional interventions remains a major issue because the expected benefit depends on the actual intake. Seemingly, obvious reasons could not be retained as valid explanations. Compliance seems thus to be primarily a question of will and information; the importance of nutritional supplementation needs to be emphasized by specific patients' education.

Effect of selective recording on estimates of heritability

En este trabajo se analiza el efecto de la selección de datos sobre las estimaciones de heredabilidad. Se estimó el valor de heredabilidad del tamaño de camada en una población porcina en la que los datos correspondientes a las cerdas más viejas eran una muestra seleccionada. Las estimaciones se obtuvieron usando distintos conjuntos de datos derivados de toda la información disponible. Esos conjunto de datos se compararon evaluando su capacidad predictiva. Se vio que las estimaciones de heredabilidad obtenidas utilizando todos los datos disponibles correspondían a valores infraestimados. También se simuló un carácter materno y se generó un conjunto de datos seleccionados eliminando aquellos correspondientes a las hembras sin padres conocidos. Distintos modelos, habitualmente empleados cuando no existe selección de registros, se consideraron para estimar el valor de heredabilidad. Los resultados mostraron que ninguno de esos modelos ofrecía estimaciones insesgadas. Sólo los modelos que tenían en cuenta el efecto de la selección sobre la media residual y la media y varianza genéticas ofrecían estimaciones poco sesgadas. Sin embargo, para poder aplicarlos se debe conocer la selección realizada. El problema de la selección de datos es difícil de abordar cuando se desconoce cual es el proceso de selección que se ha realizado en una población.

COMPASS identifies T-cell subsets correlated with clinical outcomes.

Advances in flow cytometry and other single-cell technologies have enabled high-dimensional, high-throughput measurements of individual cells as well as the interrogation of cell population heterogeneity. However, in many instances, computational tools to analyze the wealth of data generated by these technologies are lacking. Here, we present a computational framework for unbiased combinatorial polyfunctionality analysis of antigen-specific T-cell subsets (COMPASS). COMPASS uses a Bayesian hierarchical framework to model all observed cell subsets and select those most likely to have antigen-specific responses. Cell-subset responses are quantified by posterior probabilities, and human subject-level responses are quantified by two summary statistics that describe the quality of an individual's polyfunctional response and can be correlated directly with clinical outcome. Using three clinical data sets of cytokine production, we demonstrate how COMPASS improves characterization of antigen-specific T cells and reveals cellular 'correlates of protection/immunity' in the RV144 HIV vaccine efficacy trial that are missed by other methods. COMPASS is available as open-source software.

MAGIC TeV Gamma-Ray Observations of Markarian 421 during Multiwavelength Campaigns in 2006

Wide-range spectral coverage of blazar-type active galactic nuclei is of paramount importance for understanding the particle acceleration mechanisms assumed to take place in their jets. The Major Atmospheric Gamma Imaging Cerenkov (MAGIC) telescope participated in three multiwavelength (MWL) campaigns, observing the blazar Markarian (Mkn) 421 during the nights of April 28 and 29, 2006, and June 14, 2006. Aims. We analyzed the corresponding MAGIC very-high energy observations during 9 nights from April 22 to 30, 2006 and on June 14, 2006. We inferred light curves with sub-day resolution and night-by-night energy spectra. Methods. MAGIC detects γ-rays by observing extended air showers in the atmosphere. The obtained air-shower images were analyzed using the standard MAGIC analysis chain. Results. A strong γ-ray signal was detected from Mkn 421 on all observation nights. The flux (E > 250 GeV) varied on night-by-night basis between (0.92±0.11) × 10-10 cm-2 s-1 (0.57 Crab units) and (3.21±0.15) × 10-10 cm-2 s-1 (2.0 Crab units) in April 2006. There is a clear indication for intra-night variability with a doubling time of 36± min on the night of April 29, 2006, establishing once more rapid flux variability for this object. For all individual nights γ-ray spectra could be inferred, with power-law indices ranging from 1.66 to 2.47. We did not find statistically significant correlations between the spectral index and the flux state for individual nights. During the June 2006 campaign, a flux substantially lower than the one measured by the Whipple 10-m telescope four days later was found. Using a log-parabolic power law fit we deduced for some data sets the location of the spectral peak in the very-high energy regime. Our results confirm the indications of rising peak energy with increasing flux, as expected in leptonic acceleration models.

Life-time growth patterns of pumpkinseed Lepomis gibbosus introduced to Europe, relative to North American populations

The pumpkinseed Lepomis gibbosus, an omnivorous, nest guarding North American sunfish, was introduced into European waters about 100 years ago. To assess growth performance following introduction, we reviewed the available data for North American and European populations of pumpkinseed and compared the back-calculated age-specific growth for juveniles (standard length, SL, at age two) and adults (age two to five increment) as well as adult body size (SL at age five), von Bertalanffy growth model parameters and the index of growth (in length) performance (φ′). For continental comparisons of growth trajectory, mean growth curves for North American and Europe were calculated with the von Bertalanffy model using pooled data sets for each continent. Juvenile growth rate did not differ between European and North American pumpkinseed, but mean adult body size and adult growth rate were both significantly greater in North American than European populations. Adult body size decreased with increasing latitude (ANOVA) in North American populations, but this was not observed with adult growth rate. In contrast, adult body size tended to increase with latitude in European populations. Adult body size correlated significantly with φ′. The von Bertalanffy model described the overall growth patterns of North American and European populations reasonably well, but on the individual population level, length asymptotes were unrealistic (estimates that were > 20 % of the mean back-calculated size for the oldest age class) for a third of European populations and 80% of the North American populations. In contrast to North American pumpkinseed populations, somatic growth in European populations appears to be compromised by limited, but adequate, food resources, probably due to strong intraspecific interactions. This appears to be especially acute in adults, having potential ramifications for life span and reproductive allocation