"A Primitive Kind of Superstition": The Idea of the Paranoid Style in Art, Psychiatry, and Politics.

Popularized by Richard Hofstadter, the notion of "paranoid style" is the most influential attempt at applying the category of paranoia to the study of politics. Yet, the success of this elegant formula conceals a complex history and a set of unarticulated assumptions about the connections between symbolic phenomena, psychopathological states, and politics. The article proceeds to recover these assumptions and suggests that the notion of "paranoid style" is ultimately indeterminate, making its application arbitrary and ideological.

Paramedical students' perceptions of research: a survey.

BACKGROUND: There is a general perception that research is underdeveloped in rehabilitation professions. However, a PubMed search found that the growth in publications in the rehabilitation field was twice that of the general medical field. Despite this growth, another study focusing on Europe found that the proportion of articles reporting on clinical research in the rehabilitation field remained low (less than 40% of articles). This could be due to lack of teaching about research in rehabilitation schools or the late introduction of such courses. AIMS: Describe the students' perceptions of research: their desire to conduct research, the usefulness of research and research competence. METHODS: Questionnaire survey targeting all French paramedical students (speech therapy, occupational therapy, psychomotricity, audiometry, physiotherapy, orthoptics) in their final year of study in 2018-2019. RESULTS: Overall, 791 students completed the full survey representing a response rate of 36.3% of the students contacted. Only 34.3% of rehabilitation students were willing to conduct research despite finding it useful (98.6%). The main barrier was the preference for their core operational work (cited 444 times, representing 17.6% of citations). There was a significant relation between perceived competence and the attractiveness of research: 84% of the students not interested in research felt they were not competent to conduct research but this figure dropped to 57.6% amongst the students interested in research (OR 4.0; 95% CI 2.9-5.6). Using a multivariate analysis, we confirmed that the main incentive was feeling competent, as well as past contact with research and supervisors who promoted research work. CONCLUSION: Students have little contact with research during their internships, low perceived competence and, consequently, little desire to conduct research.

Linking the International Wheat Genome Sequencing Consortium bread wheat reference genome sequence to wheat genetic and phenomic data.

The Wheat@URGI portal has been developed to provide the international community of researchers and breeders with access to the bread wheat reference genome sequence produced by the International Wheat Genome Sequencing Consortium. Genome browsers, BLAST, and InterMine tools have been established for in-depth exploration of the genome sequence together with additional linked datasets including physical maps, sequence variations, gene expression, and genetic and phenomic data from other international collaborative projects already stored in the GnpIS information system. The portal provides enhanced search and browser features that will facilitate the deployment of the latest genomics resources in wheat improvement.

Structural and functional partitioning of bread wheat chromosome 3B.

We produced a reference sequence of the 1-gigabase chromosome 3B of hexaploid bread wheat. By sequencing 8452 bacterial artificial chromosomes in pools, we assembled a sequence of 774 megabases carrying 5326 protein-coding genes, 1938 pseudogenes, and 85% of transposable elements. The distribution of structural and functional features along the chromosome revealed partitioning correlated with meiotic recombination. Comparative analyses indicated high wheat-specific inter- and intrachromosomal gene duplication activities that are potential sources of variability for adaption. In addition to providing a better understanding of the organization, function, and evolution of a large and polyploid genome, the availability of a high-quality sequence anchored to genetic maps will accelerate the identification of genes underlying important agronomic traits.

TriAnnot: A Versatile and High Performance Pipeline for the Automated Annotation of Plant Genomes.

In support of the international effort to obtain a reference sequence of the bread wheat genome and to provide plant communities dealing with large and complex genomes with a versatile, easy-to-use online automated tool for annotation, we have developed the TriAnnot pipeline. Its modular architecture allows for the annotation and masking of transposable elements, the structural, and functional annotation of protein-coding genes with an evidence-based quality indexing, and the identification of conserved non-coding sequences and molecular markers. The TriAnnot pipeline is parallelized on a 712 CPU computing cluster that can run a 1-Gb sequence annotation in less than 5 days. It is accessible through a web interface for small scale analyses or through a server for large scale annotations. The performance of TriAnnot was evaluated in terms of sensitivity, specificity, and general fitness using curated reference sequence sets from rice and wheat. In less than 8 h, TriAnnot was able to predict more than 83% of the 3,748 CDS from rice chromosome 1 with a fitness of 67.4%. On a set of 12 reference Mb-sized contigs from wheat chromosome 3B, TriAnnot predicted and annotated 93.3% of the genes among which 54% were perfectly identified in accordance with the reference annotation. It also allowed the curation of 12 genes based on new biological evidences, increasing the percentage of perfect gene prediction to 63%. TriAnnot systematically showed a higher fitness than other annotation pipelines that are not improved for wheat. As it is easily adaptable to the annotation of other plant genomes, TriAnnot should become a useful resource for the annotation of large and complex genomes in the future.

Cyborg pantocrator: international relations theory from decisionism to rational choice.

International relations theory took shape in the 1950s in reaction to the behavioral social science movement, emphasizing the limits of rationality in a context of high uncertainty, weak rules, and the possibility of lethal conflict. Yet the same discipline rapidly developed "rational choice" models applied to foreign policy decision making or nuclear strategy. This paper argues that this transformation took place almost seamlessly around the concept of "decision." Initially associated with an antirationalist or "decisionist" approach to politics, the sovereign decision became the epitome of political rationality when it was redescribed as "rational choice," thus easing the cultural acceptance of political realism in the postwar years.

Ancestral grass karyotype reconstruction unravels new mechanisms of genome shuffling as a source of plant evolution.

The comparison of the chromosome numbers of today's species with common reconstructed paleo-ancestors has led to intense speculation of how chromosomes have been rearranged over time in mammals. However, similar studies in plants with respect to genome evolution as well as molecular mechanisms leading to mosaic synteny blocks have been lacking due to relevant examples of evolutionary zooms from genomic sequences. Such studies require genomes of species that belong to the same family but are diverged to fall into different subfamilies. Our most important crops belong to the family of the grasses, where a number of genomes have now been sequenced. Based on detailed paleogenomics, using inference from n = 5-12 grass ancestral karyotypes (AGKs) in terms of gene content and order, we delineated sequence intervals comprising a complete set of junction break points of orthologous regions from rice, maize, sorghum, and Brachypodium genomes, representing three different subfamilies and different polyploidization events. By focusing on these sequence intervals, we could show that the chromosome number variation/reduction from the n = 12 common paleo-ancestor was driven by nonrandom centric double-strand break repair events. It appeared that the centromeric/telomeric illegitimate recombination between nonhomologous chromosomes led to nested chromosome fusions (NCFs) and synteny break points (SBPs). When intervals comprising NCFs were compared in their structure, we concluded that SBPs (1) were meiotic recombination hotspots, (2) corresponded to high sequence turnover loci through repeat invasion, and (3) might be considered as hotspots of evolutionary novelty that could act as a reservoir for producing adaptive phenotypes.

Reconstruction of monocotelydoneous proto-chromosomes reveals faster evolution in plants than in animals.

Paleogenomics seeks to reconstruct ancestral genomes from the genes of today's species. The characterization of paleo-duplications represented by 11,737 orthologs and 4,382 paralogs identified in five species belonging to three of the agronomically most important subfamilies of grasses, that is, Ehrhartoideae (rice) Panicoideae (sorghum, maize), and Pooideae (wheat, barley), permitted us to propose a model for an ancestral genome with a minimal size of 33.6 Mb structured in five proto-chromosomes containing at least 9,138 predicted proto-genes. It appears that only four major evolutionary shuffling events (alpha, beta, gamma, and delta) explain the divergence of these five cereal genomes during their evolution from a common paleo-ancestor. Comparative analysis of ancestral gene function with rice as a reference indicated that five categories of genes were preferentially modified during evolution. Furthermore, alignments between the five grass proto-chromosomes and the recently identified seven eudicot proto-chromosomes indicated that additional very active episodes of genome rearrangements and gene mobility occurred during angiosperm evolution. If one compares the pace of primate evolution of 90 million years (233 species) to 60 million years of the Poaceae (10,000 species), change in chromosome structure through speciation has accelerated significantly in plants.

Genomics in cereals: from genome-wide conserved orthologous set (COS) sequences to candidate genes for trait dissection.

Recent updates in comparative genomics among cereals have provided the opportunity to identify conserved orthologous set (COS) DNA sequences for cross-genome map-based cloning of candidate genes underpinning quantitative traits. New tools are described that are applicable to any cereal genome of interest, namely, alignment criterion for orthologous couples identification, as well as the Intron Spanning Marker software to automatically select intron-spanning primer pairs. In order to test the software, it was applied to the bread wheat genome, and 695 COS markers were assigned to 1,535 wheat loci (on average one marker/2.6 cM) based on 827 robust rice-wheat orthologs. Furthermore, 31 of the 695 COS markers were selected to fine map a pentosan viscosity quantitative trait loci (QTL) on wheat chromosome 7A. Among the 31 COS markers, 14 (45%) were polymorphic between the parental lines and 12 were mapped within the QTL confidence interval with one marker every 0.6 cM defining candidate genes among the rice orthologous region.

Toward a transnational history of the social sciences.

Historical accounts of the social sciences have too often accepted local or national institutions as a self-evident framework of analysis, instead of considering them as being embedded in transnational relations of various kinds. Evolving patterns of transnational mobility and exchange cut through the neat distinction between the local, the national, and the inter-national, and thus represent an essential component in the dynamics of the social sciences, as well as a fruitful perspective for rethinking their historical development. In this programmatic outline, it is argued that a transnational history of the social sciences may be fruitfully understood on the basis of three general mechanisms, which have structured the transnational flows of people and ideas in decisive ways: (a) the functioning of international scholarly institutions, (b) the transnational mobility of scholars, and (c) the politics of trans-national exchange of nonacademic institutions. The article subsequently examines and illustrates each of these mechanisms.

Physical mapping in large genomes: accelerating anchoring of BAC contigs to genetic maps through in silico analysis.

Anchored physical maps represent essential frameworks for map-based cloning, comparative genomics studies, and genome sequencing projects. High throughput anchoring can be achieved by polymerase chain reaction (PCR) screening of bacterial artificial chromosome (BAC) library pools with molecular markers. However, for large genomes such as wheat, the development of high dimension pools and the number of reactions that need to be performed can be extremely large making the screening laborious and costly. To improve the cost efficiency of anchoring in such large genomes, we have developed a new software named Elephant (electronic physical map anchoring tool) that combines BAC contig information generated by FingerPrinted Contig with results of BAC library pools screening to identify BAC addresses with a minimal amount of PCR reactions. Elephant was evaluated during the construction of a physical map of chromosome 3B of hexaploid wheat. Results show that a one dimensional pool screening can be sufficient to anchor a BAC contig while reducing the number of PCR by 384-fold thereby demonstrating that Elephant is an efficient and cost-effective tool to support physical mapping in large genomes.

Characterization of the GATC regulatory network in E. coli.

BACKGROUND: The tetranucleotide GATC is methylated in Escherichia. coli by the DNA methyltransferase (Dam) and is known to be implicated in numerous cellular processes. Mutants lacking Dam are characterized by a pleiotropic phenotype. The existence of a GATC regulated network, thought to be involved in cold and oxygen shift, had been proposed and its existence has recently been confirmed. The aim of this article is to describe the components of the GATC regulated network of E. coli in detail and propose a role of this network in the light of an evolutionary advantage for the organism. RESULTS: We have classified the genes of the GATC network according to the EcoCyc functional classes. Comparisons with all of E. coli's genes and the genes involved in the SOS and stress response show that the GATC network forms a group apart. The functional classes that characterize the network are the Energy metabolism (in particular respiration), Fatty acid/ Phospholipid metabolism and Nucleotide metabolism. CONCLUSIONS: The network is thought to come into play when the cell undergoes coldshock and is likely to enter stationary phase.The respiration is almost completely under GATC control and according to our hypothesis it will be blocked at the moment of coldshock; this might give the cell a selective advantage as it increases its chances for survival when entering stationary phase under coldshock. We predict the accumulation of formate and possibly succinate, which might increase the cell's resistance, in this case to antimicrobial agents, when entering stationary phase.

The difficult interpretation of transcriptome data: the case of the GATC regulatory network.

Genomic analyses on part of Escherichia coli's chromosome had suggested the existence of a GATC regulated network. This has recently been confirmed through a transcriptome analysis. Two hypotheses about the molecular control mechanism have been proposed-(i) the GATC network regulation is caused by the presence of GATC clusters within the coding sequences; the regulation is the direct consequence of the clusters' hemi-methylation and therefore their elevated melting temperature, (ii) the regulation is caused by the presence of GATCs in the non-coding 500 bp upstream regions of the affected genes; it is the consequence of an interaction with a regulatory protein like Fnr or CAP. An analysis of the transcriptome data has not allowed us to decide between the two hypotheses. We have therefore taken a classic genomic approach, analyzing the statistical distribution of GATC along the chromosome, using a realistic model of the chromosome as theoretical reference. We observe no particular distribution of GATC in the non-coding upstream regions; however, we confirm the presence of GATC clusters within the genes. In order to verify that the particular distribution observed in E. coli is not a statistical artefact, but has a physiological role, we have carried out the same analysis on Salmonella, making the hypothesis that the genes containing a GATC clusters should be largely the same in the two bacteria. This has been indeed observed, showing that the genes containing a GATC cluster are part of a regulation network. The present is a case study, which demonstrates that the analysis of transcriptome data does not always permit to identify the primary cause of a phenomenon observed; on the other hand, a classic genomic approach linked with a comparative study of related genomes may allow this identification.