War and Natural Resource Exploitation

We build a theoretical framework that allows for endogenous conflict behaviour (i.e., fighting efforts) and for endogenous natural resource exploitation (i.e., speed, ownership, and investments). While depletion is spread in a balanced Hotelling fashion during peace, the presence of conflict creates incentives for rapacious extraction, as this lowers the stakes of future contest. This voracious extraction depresses total oil revenue, especially if world oil demand is relatively elastic and the government's weapon advantage is weak. Some of these political distortions can be overcome by bribing rebels or by government investment in weapons. The shadow of conflict can also make less efficient nationalized oil extraction more attractive than private extraction, as insecure property rights create a holdup problem for the private firm and lead to a lower license fee. Furthermore, the government fights less intensely than the rebels under private exploitation, which leads to more government turnover. Without credible commitment to future fighting efforts, private oil depletion is only lucrative if the government's non-oil office rents are large and weaponry powerful, which guarantees the government a stronger grip on office and makes the holdup problem less severe.

The Universal Protein Resource (UniProt) in 2010.

The primary mission of UniProt is to support biological research by maintaining a stable, comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross-references and querying interfaces freely accessible to the scientific community. UniProt is produced by the UniProt Consortium which consists of groups from the European Bioinformatics Institute (EBI), the Swiss Institute of Bioinformatics (SIB) and the Protein Information Resource (PIR). UniProt is comprised of four major components, each optimized for different uses: the UniProt Archive, the UniProt Knowledgebase, the UniProt Reference Clusters and the UniProt Metagenomic and Environmental Sequence Database. UniProt is updated and distributed every 3 weeks and can be accessed online for searches or download at http://www.uniprot.org.

Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation.

The international Functional Annotation Of the Mammalian Genomes 4 (FANTOM4) research collaboration set out to better understand the transcriptional network that regulates macrophage differentiation and to uncover novel components of the transcriptome employing a series of high-throughput experiments. The primary and unique technique is cap analysis of gene expression (CAGE), sequencing mRNA 5'-ends with a second-generation sequencer to quantify promoter activities even in the absence of gene annotation. Additional genome-wide experiments complement the setup including short RNA sequencing, microarray gene expression profiling on large-scale perturbation experiments and ChIP-chip for epigenetic marks and transcription factors. All the experiments are performed in a differentiation time course of the THP-1 human leukemic cell line. Furthermore, we performed a large-scale mammalian two-hybrid (M2H) assay between transcription factors and monitored their expression profile across human and mouse tissues with qRT-PCR to address combinatorial effects of regulation by transcription factors. These interdependent data have been analyzed individually and in combination with each other and are published in related but distinct papers. We provide all data together with systematic annotation in an integrated view as resource for the scientific community (http://fantom.gsc.riken.jp/4/). Additionally, we assembled a rich set of derived analysis results including published predicted and validated regulatory interactions. Here we introduce the resource and its update after the initial release.

L'hypnose: une ressource en soins palliatifs? Etude qualitative sur l'apport de l'hypnose chez des patients oncologique.s [Hypnosis as a resource in palliative care. A qualitative study of the contribution of hypnosis to the care of oncology patients].

Hypnosis is recognised in medicine as an effective complementary therapy. However, few qualitative data are available concerning the benefits it may bring. This qualitative exploratory study aimed to examine the contribution of hypnosis to the care of advanced cancer patients. Results demonstrate that hypnosis is an effective and efficient means of developing the resources of people suffering from serious illness. After an average of four hypnotherapy sessions, patients said they were able to locate previously unexploited resources within themselves and were able to become autonomous in the use of self-hypnosis. The major benefit reported concerned a reduction in anxiety. For patients experiencing anxiety about death, hypnosis allowed them, within a therapeutic environment perceived as safe, to explore different facets of their fears and to develop adaptive strategies. Aside from slight fatigue experienced during the sessions, no adverse side-effects were reported. In conclusion, this study exploring the effects of hypnosis allowed us to identify important benefits for patients suffering from advanced cancer. Consequently, replication on a larger scale is recommended in order to ascertain the extent to which it is possible to generalise from these results and in order better to define the characteristics of patients most likely to benefit from this therapy.

Different arbuscular mycorrhizal fungi alter coexistence and resource distribution between co-occurring plants

It is often thought that the coexistence of plants and plant diversity is determined by resource heterogeneity of the abiotic environment. However, the presence and heterogeneity of biotic plant resources, such as arbuscular mycorrhizal fungi (AMF), could also affect plant species coexistence. In this study, Brachypodium pinnatum and Prunella vulgaris were grown together in pots and biotic resource heterogeneity was simulated by inoculating these pots with one of three different AMF taxa, with a mixture of these three taxa, or pots remained uninoculated. The AMF acted as biotic plant resources since the biomass of plants in pots inoculated with AMF was on average 11.8 times higher than uninoculated pots. The way in which the two plant species coexisted, and the distribution of phosphorus and nitrogen between the plant species, varied strongly depending on which AMF were present. The results showed that the composition of AMF communities determines how plant species coexist and to which plant species nutrients are allocated. Biotic plant resources such as AMF should therefore be considered as one of the factors that determine how plant species coexist and how soil resources are distributed among co-occurring plant species.

Prise en charge d'adolescents souffrant d'anorexie mentale: le rôle des parents, une approche basée sur l'évidence [Adolescents with an eating disorder: an evidence-based approach on the role of parents].

L'adolescence est une période de grands changements et de ce fait potentiellement de grande vulnérabilité. Ainsi, les bouleversements physiques et psychiques induits par les processus pubertaires sont un terrain propice à l'émergence d'un trouble des conduites alimentaires (TCA). La thérapie familiale selon Maudsley, ou family based treatment (FBT), a émergé en parallèle aux avancées neurobiologiques, qui confirment une origine multifactorielle des troubles du comportement alimentaire. Cette thérapie replace les parents au centre de la prise en charge des adolescents souffrant d'un TCA avec comme grand atout, une approche basée sur l'évidence scientifique. Adolescence is a time of great change and therefore, potentially of great vulnerability. Thus, physical and psychological changes induced by pubertal processes are fertile ground for the emergence of an eating disorder (ED). Family therapy according to Maudsley or "family based treatment" (FBT) has emerged in parallel with neurobiological advances confirming a multifactorial origin of eating disorders. This therapy places parents at the centre of care for adolescents with EDs. Its great asset is the evidence-based approach underpinning the therapy.

Probabilistic base calling of Solexa sequencing data.

BACKGROUND: Solexa/Illumina short-read ultra-high throughput DNA sequencing technology produces millions of short tags (up to 36 bases) by parallel sequencing-by-synthesis of DNA colonies. The processing and statistical analysis of such high-throughput data poses new challenges; currently a fair proportion of the tags are routinely discarded due to an inability to match them to a reference sequence, thereby reducing the effective throughput of the technology. RESULTS: We propose a novel base calling algorithm using model-based clustering and probability theory to identify ambiguous bases and code them with IUPAC symbols. We also select optimal sub-tags using a score based on information content to remove uncertain bases towards the ends of the reads. CONCLUSION: We show that the method improves genome coverage and number of usable tags as compared with Solexa's data processing pipeline by an average of 15%. An R package is provided which allows fast and accurate base calling of Solexa's fluorescence intensity files and the production of informative diagnostic plots.

Tree-based message diffusion for managing replicated data in unreliable and resource-constrained peer-to-peer environment

Abstract This thesis proposes a set of adaptive broadcast solutions and an adaptive data replication solution to support the deployment of P2P applications. P2P applications are an emerging type of distributed applications that are running on top of P2P networks. Typical P2P applications are video streaming, file sharing, etc. While interesting because they are fully distributed, P2P applications suffer from several deployment problems, due to the nature of the environment on which they perform. Indeed, defining an application on top of a P2P network often means defining an application where peers contribute resources in exchange for their ability to use the P2P application. For example, in P2P file sharing application, while the user is downloading some file, the P2P application is in parallel serving that file to other users. Such peers could have limited hardware resources, e.g., CPU, bandwidth and memory or the end-user could decide to limit the resources it dedicates to the P2P application a priori. In addition, a P2P network is typically emerged into an unreliable environment, where communication links and processes are subject to message losses and crashes, respectively. To support P2P applications, this thesis proposes a set of services that address some underlying constraints related to the nature of P2P networks. The proposed services include a set of adaptive broadcast solutions and an adaptive data replication solution that can be used as the basis of several P2P applications. Our data replication solution permits to increase availability and to reduce the communication overhead. The broadcast solutions aim, at providing a communication substrate encapsulating one of the key communication paradigms used by P2P applications: broadcast. Our broadcast solutions typically aim at offering reliability and scalability to some upper layer, be it an end-to-end P2P application or another system-level layer, such as a data replication layer. Our contributions are organized in a protocol stack made of three layers. In each layer, we propose a set of adaptive protocols that address specific constraints imposed by the environment. Each protocol is evaluated through a set of simulations. The adaptiveness aspect of our solutions relies on the fact that they take into account the constraints of the underlying system in a proactive manner. To model these constraints, we define an environment approximation algorithm allowing us to obtain an approximated view about the system or part of it. This approximated view includes the topology and the components reliability expressed in probabilistic terms. To adapt to the underlying system constraints, the proposed broadcast solutions route messages through tree overlays permitting to maximize the broadcast reliability. Here, the broadcast reliability is expressed as a function of the selected paths reliability and of the use of available resources. These resources are modeled in terms of quotas of messages translating the receiving and sending capacities at each node. To allow a deployment in a large-scale system, we take into account the available memory at processes by limiting the view they have to maintain about the system. Using this partial view, we propose three scalable broadcast algorithms, which are based on a propagation overlay that tends to the global tree overlay and adapts to some constraints of the underlying system. At a higher level, this thesis also proposes a data replication solution that is adaptive both in terms of replica placement and in terms of request routing. At the routing level, this solution takes the unreliability of the environment into account, in order to maximize reliable delivery of requests. At the replica placement level, the dynamically changing origin and frequency of read/write requests are analyzed, in order to define a set of replica that minimizes communication cost.

Ongoing and future developments at the Universal Protein Resource.

The primary mission of Universal Protein Resource (UniProt) is to support biological research by maintaining a stable, comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross-references and querying interfaces freely accessible to the scientific community. UniProt is produced by the UniProt Consortium which consists of groups from the European Bioinformatics Institute (EBI), the Swiss Institute of Bioinformatics (SIB) and the Protein Information Resource (PIR). UniProt is comprised of four major components, each optimized for different uses: the UniProt Archive, the UniProt Knowledgebase, the UniProt Reference Clusters and the UniProt Metagenomic and Environmental Sequence Database. UniProt is updated and distributed every 4 weeks and can be accessed online for searches or download at http://www.uniprot.org.

Cancers cutanés envahissant la base du crâne [Skin cancers infiltrating the skull base].

Squamous cell and basocellular carcinoma of the face have an excellent prognosis. Nevertherless, a small proportion therefore of these cancers differs by a much more aggressive behavior, caracterised by a tendency to infiltrate the deep facial soft tissues and facial bones. The invasion of the craniofacial skeleton and the intracranial structures follows the embryonic fusion lines or the facial sensitive or motor nerves, sometimes years after the initial treatment. The development of craniofacial surgery, reconstruction techniques and conformational radiotherapy allows us now to offer curative guided treatments, for these advanced staged tumors with a remaining limited prognosis. A therapeutic benefit implies a rigorous selection of these patients.

Psychiatrie de l'enfant et de l'adolescent : une approche basée sur les preuves

L'approche basée sur les preuves, dérivée de I'evidence based medicine anglo-saxonne, offre une vision élargie de la pédopsychiatrie en permettant aux thérapeutes de s'extraire de la stricte soumission aux conclusions de la recherche pour donner à la pratique, dans une certaine mesure, la possibilité de valider des choix de prise en charge pluridisciplinaires. Alors que l'evidence based médecine s'est imposée dans la plupart des spécialités médicales, elle tarde à s'implanter en psychiatrie de l'enfant et de l'adolescent. Cet ouvrage fait donc le point sur les connaissances actuelles et propose une approche plus globale fondée sur les preuves. Les 13 chapitres qui le composent couvrent une grande partie des troubles pédopsychiatriques en y intégrant des sujets d'ouverture comme l'alliance thérapeutique, les soins sous contrainte ou les équipes mobiles. Un chapitre consacré aux médicaments psychotropes utilisés chez l'enfant et l'adolescent permet d'offrir un aperçu complet des moyens thérapeutiques à disposition pour chacun de ces troubles.