Crystal structure of yeast peroxisomal multifunctional enzyme: structural basis for substrate specificity of (3R)-hydroxyacyl-CoA dehydrogenase units.

(3R)-hydroxyacyl-CoA dehydrogenase is part of multifunctional enzyme type 2 (MFE-2) of peroxisomal fatty acid beta-oxidation. The MFE-2 protein from yeasts contains in the same polypeptide chain two dehydrogenases (A and B), which possess difference in substrate specificity. The crystal structure of Candida tropicalis (3R)-hydroxyacyl-CoA dehydrogenase AB heterodimer, consisting of dehydrogenase A and B, determined at the resolution of 2.2A, shows overall similarity with the prototypic counterpart from rat, but also important differences that explain the substrate specificity differences observed. Docking studies suggest that dehydrogenase A binds the hydrophobic fatty acyl chain of a medium-chain-length ((3R)-OH-C10) substrate as bent into the binding pocket, whereas the short-chain substrates are dislocated by two mechanisms: (i) a short-chain-length 3-hydroxyacyl group ((3R)-OH-C4) does not reach the hydrophobic contacts needed for anchoring the substrate into the active site; and (ii) Leu44 in the loop above the NAD(+) cofactor attracts short-chain-length substrates away from the active site. Dehydrogenase B, which can use a (3R)-OH-C4 substrate, has a more shallow binding pocket and the substrate is correctly placed for catalysis. Based on the current structure, and together with the structure of the 2-enoyl-CoA hydratase 2 unit of yeast MFE-2 it becomes obvious that in yeast and mammalian MFE-2s, despite basically identical functional domains, the assembly of these domains into a mature, dimeric multifunctional enzyme is very different.

The Impact of Digitization on the Management of Administrative Procedures : The Case of Building Permits

Information and Communication Technologies provide public administrations new ways to meet their users' needs. At the same time, e-Government practices support the public sector in improving the quality of service provision and of its internal operations. In this paper we discuss the impacts of digitization on the management of administrative procedures. The theoretical framework and the research model that we will use in this study help us tackle the question of how digitization transforms administrative procedures as, for example, in terms of time and roles. The multiplicity of institutions involved in issuing building permits led us to consider this administrative procedure as a very interesting case study. An online survey was first addressed to Swiss civil servants to explore the field, and here we present some of its results. We are currently undertaking an in-depth case study of the building permit procedures in three Swiss Cantons, which we will also present in this paper. We will conclude with a discussion and the future steps of this project.

A unique Permian-Triassic boundary section from the Neotethyan Hawasina Basin, Central Oman Mountains

In the Wadi Wasit area (Central Oman Mountains), Dienerian breccias are widespread. These breccias consist mostly of Guadalupian reefal blocks, often dolomitised, and some rare small-sized blocks of lowermost Triassic bivalve-bearing limestones. A unique block, with a size of about 200 m(3), including Permian and earliest Triassic faunas has been studied in detail. The so-called Wadi Wasit block consists of three major lithological units. A basal unstratified grey limestone is rich in various reef-building organisms (rugose corals, calcareous sponges, stromatoporoids) and has been dated as Middle Permian. It is disconformably overlain by well- and thin-bedded light grey to yellowish coloured limestones rich in molluscs. Two major lithologies (Coquina Limestone respectively Bioclastic Limestone unit) characterise the shelly limestones, their contact seems gradual. These two units are well-dated; they are of Griesbachian age and contain three conodont zones, the Parvus Zone, the Staeschei Zone and the Sosioensis Zone, and two ammonoid zones, the Ophiceras tibeticum Zone and an 'unnamed interval'. The third unit consists of a grey marly limestone containing Neospathodus kummeli (basal Dienerian). It is the first record of well-dated basal Triassic sediments in the Arabian Peninsula. The Coquina Limestone is dominated by the bivalve Promyalina with some Claraia and Eumorphotis. This bivalve association is interpreted as a pioneering opportunistic assemblage. Towards the top of the Bioclastic Limestone unit, the faunal diversity increases and contains probably more than 20 taxa of bivalves, microgastropods, crinoids, brachiopods, ammonoids, echinoid spines, ostracods and conodonts. The generic diversity of this biofacies exceeds by far any other Griesbachian assemblage known. Our data give new evidence for the geodynamical history for the distal carbonate shelf bordering the Hawasina Basin. A break in the sedimentation characterises the Late Permian. The basal Triassic shows a steady transgression and the breccias may record a distinct gravitational collapse of platform margins linked with sea-level low stand at the end of Induan time (late Dienerian-basal Smithian). delta(13)C(carb) isotopic analyses were performed and yield typical Permian values of around 4parts per thousand for the Reefal Limestone, with a strong negative shift across the Permian-Triassic boundary. During the Griesbachian values shift positively from 0.5 to 3.1parts per thousand parallel to an increase in faunal diversity and probably primary productivity. The detailed faunal analysis and the discovery of an unexpected diversity give,us a new understanding of the recovery of the Early Triassic marine ecosystem.

Apprentissage automatique de la morphologie : le cas des structures racine-schème

RÉSUMÉ Cette thèse porte sur le développement de méthodes algorithmiques pour découvrir automatiquement la structure morphologique des mots d'un corpus. On considère en particulier le cas des langues s'approchant du type introflexionnel, comme l'arabe ou l'hébreu. La tradition linguistique décrit la morphologie de ces langues en termes d'unités discontinues : les racines consonantiques et les schèmes vocaliques. Ce genre de structure constitue un défi pour les systèmes actuels d'apprentissage automatique, qui opèrent généralement avec des unités continues. La stratégie adoptée ici consiste à traiter le problème comme une séquence de deux sous-problèmes. Le premier est d'ordre phonologique : il s'agit de diviser les symboles (phonèmes, lettres) du corpus en deux groupes correspondant autant que possible aux consonnes et voyelles phonétiques. Le second est de nature morphologique et repose sur les résultats du premier : il s'agit d'établir l'inventaire des racines et schèmes du corpus et de déterminer leurs règles de combinaison. On examine la portée et les limites d'une approche basée sur deux hypothèses : (i) la distinction entre consonnes et voyelles peut être inférée sur la base de leur tendance à alterner dans la chaîne parlée; (ii) les racines et les schèmes peuvent être identifiés respectivement aux séquences de consonnes et voyelles découvertes précédemment. L'algorithme proposé utilise une méthode purement distributionnelle pour partitionner les symboles du corpus. Puis il applique des principes analogiques pour identifier un ensemble de candidats sérieux au titre de racine ou de schème, et pour élargir progressivement cet ensemble. Cette extension est soumise à une procédure d'évaluation basée sur le principe de la longueur de description minimale, dans- l'esprit de LINGUISTICA (Goldsmith, 2001). L'algorithme est implémenté sous la forme d'un programme informatique nommé ARABICA, et évalué sur un corpus de noms arabes, du point de vue de sa capacité à décrire le système du pluriel. Cette étude montre que des structures linguistiques complexes peuvent être découvertes en ne faisant qu'un minimum d'hypothèses a priori sur les phénomènes considérés. Elle illustre la synergie possible entre des mécanismes d'apprentissage portant sur des niveaux de description linguistique distincts, et cherche à déterminer quand et pourquoi cette coopération échoue. Elle conclut que la tension entre l'universalité de la distinction consonnes-voyelles et la spécificité de la structuration racine-schème est cruciale pour expliquer les forces et les faiblesses d'une telle approche. ABSTRACT This dissertation is concerned with the development of algorithmic methods for the unsupervised learning of natural language morphology, using a symbolically transcribed wordlist. It focuses on the case of languages approaching the introflectional type, such as Arabic or Hebrew. The morphology of such languages is traditionally described in terms of discontinuous units: consonantal roots and vocalic patterns. Inferring this kind of structure is a challenging task for current unsupervised learning systems, which generally operate with continuous units. In this study, the problem of learning root-and-pattern morphology is divided into a phonological and a morphological subproblem. The phonological component of the analysis seeks to partition the symbols of a corpus (phonemes, letters) into two subsets that correspond well with the phonetic definition of consonants and vowels; building around this result, the morphological component attempts to establish the list of roots and patterns in the corpus, and to infer the rules that govern their combinations. We assess the extent to which this can be done on the basis of two hypotheses: (i) the distinction between consonants and vowels can be learned by observing their tendency to alternate in speech; (ii) roots and patterns can be identified as sequences of the previously discovered consonants and vowels respectively. The proposed algorithm uses a purely distributional method for partitioning symbols. Then it applies analogical principles to identify a preliminary set of reliable roots and patterns, and gradually enlarge it. This extension process is guided by an evaluation procedure based on the minimum description length principle, in line with the approach to morphological learning embodied in LINGUISTICA (Goldsmith, 2001). The algorithm is implemented as a computer program named ARABICA; it is evaluated with regard to its ability to account for the system of plural formation in a corpus of Arabic nouns. This thesis shows that complex linguistic structures can be discovered without recourse to a rich set of a priori hypotheses about the phenomena under consideration. It illustrates the possible synergy between learning mechanisms operating at distinct levels of linguistic description, and attempts to determine where and why such a cooperation fails. It concludes that the tension between the universality of the consonant-vowel distinction and the specificity of root-and-pattern structure is crucial for understanding the advantages and weaknesses of this approach.

Building hippocampal circuits to learn and remember: insights into the development of human memory

The hippocampal formation is essential for the processing of episodic memories for autobiographical events that happen in unique spatiotemporal contexts. Interestingly, before 2 years of age, children are unable to form or store episodic memories for recall later in life, a phenomenon known as infantile amnesia. From 2 to 7 years of age, there are fewer memories than predicted based on a forgetting function alone, a phenomenon known as childhood amnesia. Here, we discuss the postnatal maturation of the primate hippocampal formation with the goal of characterizing the development of the neurobiological substrates thought to subserve the emergence of episodic memory. Distinct regions, layers and cells of the hippocampal formation exhibit different profiles of structural and molecular development during early postnatal life. The protracted period of neuronal addition and maturation in the dentate gyrus is accompanied by the late maturation of specific layers in different hippocampal regions that are located downstream from the dentate gyrus, particularly CA3. In contrast, distinct layers in several hippocampal regions, particularly CA1, which receive direct projections from the entorhinal cortex, exhibit an early maturation. In addition, hippocampal regions that are more highly interconnected with subcortical structures, including the subiculum, presubiculum, parasubiculum and CA2, mature even earlier. These findings, together with our studies of the development of human spatial memory, support the hypothesis that the differential maturation of distinct hippocampal circuits might underlie the differential emergence of specific "hippocampus-dependent" memory processes, culminating in the emergence of episodic memory concomitant with the maturation of all hippocampal circuits.

Central line sepsis in intensive care units : overview and update

Catheter-related infection remains a leading cause of nosocomial infections, particularly in intensive care units. It includes colonization of the device, skin exit-site infection and device- or catheter-related bloodstream infection. The latter represents the most frequent life-threatening associated complication of central venous catheter use and is associated with significant patient morbidity, mortality and extra hospital costs. The incidence of catheter-related bloodstream infection ranges from 2 to 14 episodes per 1000 catheter-days. On average, microbiologically-documented device-related bloodstream infections complicate from three to five per 100 central venous line uses, but they only represent the visible part of the iceberg and most clinical sepsis are nowadays considered to be catheter-related. We briefly review the pathophysiology of infection, highlighting the importance of the skin insertion site and of intravenous line hub as principal sources of colonization. Principles of therapy are reviewed. Several preventive approaches are also discussed, in particular the possible benefit of recently developed impregnated catheters. Finally, the potential positive impact of a multimodal global preventive strategy based on strict application of hygienic rules is presented.

Building the niche through time: using 13,000 years of data to predict the effects of climate change on three tree species in Europe

Aim Species distribution models (SDMs) based on current species ranges underestimate the potential distribution when projected in time and/or space. A multi-temporal model calibration approach has been suggested as an alternative, and we evaluate this using 13,000 years of data. Location Europe. Methods We used fossil-based records of presence for Picea abies, Abies alba and Fagus sylvatica and six climatic variables for the period 13,000 to 1000yr bp. To measure the contribution of each 1000-year time step to the total niche of each species (the niche measured by pooling all the data), we employed a principal components analysis (PCA) calibrated with data over the entire range of possible climates. Then we projected both the total niche and the partial niches from single time frames into the PCA space, and tested if the partial niches were more similar to the total niche than random. Using an ensemble forecasting approach, we calibrated SDMs for each time frame and for the pooled database. We projected each model to current climate and evaluated the results against current pollen data. We also projected all models into the future. Results Niche similarity between the partial and the total-SDMs was almost always statistically significant and increased through time. SDMs calibrated from single time frames gave different results when projected to current climate, providing evidence of a change in the species realized niches through time. Moreover, they predicted limited climate suitability when compared with the total-SDMs. The same results were obtained when projected to future climates. Main conclusions The realized climatic niche of species differed for current and future climates when SDMs were calibrated considering different past climates. Building the niche as an ensemble through time represents a way forward to a better understanding of a species' range and its ecology in a changing climate.

A novel approach to reducing number of sensing units for wearable gait analysis systems.

Gait analysis methods to estimate spatiotemporal measures, based on two, three or four gyroscopes attached on lower limbs have been discussed in the literature. The most common approach to reduce the number of sensing units is to simplify the underlying biomechanical gait model. In this study, we propose a novel method based on prediction of movements of thighs from movements of shanks. Datasets from three previous studies were used. Data from the first study (ten healthy subjects and ten with Parkinson's disease) were used to develop and calibrate a system with only two gyroscopes attached on shanks. Data from two other studies (36 subjects with hip replacement, seven subjects with coxarthrosis, and eight control subjects) were used for comparison with the other methods and for assessment of error compared to a motion capture system. Results show that the error of estimation of stride length compared to motion capture with the system with four gyroscopes and our new method based on two gyroscopes was close ( -0.8 ±6.6 versus 3.8 ±6.6 cm). An alternative with three sensing units did not show better results (error: -0.2 ±8.4 cm). Finally, a fourth that also used two units but with a simpler gait model had the highest bias compared to the reference (error: -25.6 ±7.6 cm). We concluded that it is feasible to estimate movements of thighs from movements of shanks to reduce number of needed sensing units from 4 to 2 in context of ambulatory gait analysis.