Decision Support to Crowdsourcing for Annotation and Transcription of Ancient Documents: The RECITAL Workshop

In the 18th century in Paris, only two public theatres could officially perform comedies: the Com{\'e}die-Fran{\c c}aise, and the Com{\'e}die-Italienne. The latter was much less well known. By studying a century of accounting registers, we aim to learn more about its successful plays, its actors, musicians, set designers, and all the small trades necessary for its operation, its administration, logistics and finances. To this end, we employ a mass of untapped and unpublished resources, the 27,544 pages of 63 daily registers available at the Biblioth{\`e}que Nationale de France (BnF). And we take a decidedly fresh look at emerging forms of creation and changes in the entertainmenteconomy. We developed the crowdsourcing platform RECITAL to collect and index the data from theregisters, following an emerging trend in Digital Humanities. RECITAL is built upon the ScribeAPI framework and it offers a fully-fledged web application to classify the pages, annotate with marks and tags, transcribe the indexed marks and even to verify the previous transcripts. We also describe a multi-level data model and to develop a series of monitoring anddecision tools to support crowdsourced data management up to their definitive form

Highly-multiplexed SNP genotyping for genetic mapping and germplasm diversity studies in pea

Background: Single Nucleotide Polymorphisms (SNPs) can be used as genetic markers for applications such as genetic diversity studies or genetic mapping. New technologies now allow genotyping hundreds to thousands of SNPs in a single reaction. In order to evaluate the potential of these technologies in pea, we selected a custom 384-SNP set using SNPs discovered in Pisum through the resequencing of gene fragments in different genotypes and by compiling genomic sequence data present in databases. We then designed an Illumina GoldenGate assay to genotype both a Pisum germplasm collection and a genetic mapping population with the SNP set. Results: We obtained clear allelic data for more than 92% of the SNPs (356 out of 384). Interestingly, the technique was successful for all the genotypes present in the germplasm collection, including those from species or subspecies different from the P. sativum ssp sativum used to generate sequences. By genotyping the mapping population with the SNP set, we obtained a genetic map and map positions for 37 new gene markers. Conclusion: Our results show that the Illumina GoldenGate assay can be used successfully for high-throughput SNP genotyping of diverse germplasm in pea. This genotyping approach will simplify genotyping procedures for association mapping or diversity studies purposes and open new perspectives in legume genomics

On the motivations for Merleau-Ponty’s ontological research

This paper attempts to clarify Merleau-Ponty’s later work by tracing a hitherto overlooked set of concerns that were of key consequence for the formulation of his ontological research. I argue that his ontology can be understood as a response to a set of problems originating in reflections on the intersubjective use of language in dialogue, undertaken in the early 1950s. His study of dialogue disclosed a structure of meaning-formation and pointed towards a theory of truth (both recurring ontological topics) that post-Phenomenology premises could not account for. A study of dialogue shows that speakers’ positions are interchangeable, that speaking subjects are active and passive in varying degrees, and that the intentional roles of subjects and objects are liable to shift or ‘transgress’ themselves. These observations anticipate the concepts of ‘reversibility’ and ‘narcissism’, his later view of activity and passivity, and his later view of intentionality, and sharpened the need to adopt an intersubjective focus in ontological research

Prendre soin, être responsable et s’accorder

Branches d’un marronnier vivant face au salon de l’auteur à Saint-Martin-de-Londres (Hérault) pendant le confinement, en exposition multiple (2020), © Jonathan Lhoir.« Qu’est-ce que signifie “apprivoiser” ? […]– C’est une chose trop oubliée, dit le renard. Ça signifie “créer des liens…”– Créer des liens ?– Bien sûr, dit le renard. Tu n’es encore pour moi qu’un petit garçon tout semblable à cent mille petits garçons. Et je n’ai pas besoin de toi. Et tu n’as pas besoin de moi non plus.Je ne su..

A positioning pillow to improve lumbar puncture success rate in paediatric haematology-oncology patients: a randomized controlled trial

<p>Abstract</p> <p>Background</p> <p>Lumbar punctures (LPs) are common in children with cancer. Although pain management during the lumbar puncture has been well standardized, dealing with stress and anxiety is not well addressed yet. Our objective was to evaluate the potential improvement of the LP success rate using a positioning pillow, to ensure maximum lumbar flexion, and allow paravertebral muscles to relax, in children who are awake, with either conscious sedation or no sedation.</p> <p>Methods</p> <p>Children aged 2–18 years undergoing LP were randomly assigned to a positioning pillow or no intervention. The primary outcome was the rate of success, i.e. achieving the LP (sampling or injection) at the first attempt, without bleeding (RBC < 50/mm³). The secondary outcomes included: the child's pain, assessed by a self-administered visual analogical scales (VAS) for children over 6 years of age; the parents' and caregivers' perception of the child's pain; the satisfaction of the children, the parents, the caregivers and the physician. The child's cooperation and the occurrence of post-LP syndrome were also evaluated.</p> <p>Results</p> <p>124 children (62 in each group) were included. The LP pillow tended to increase the success rate of LPs (67% vs. 57%, p = 0.23), and decreased the post-LP syndromes (15% vs. 24%, p = 0.17) but the differences were not statistically significant. In children over 6-year of age (n = 72), the rate of success was significantly higher in the pillow group (58.5% vs. 41.5%, p = 0.031), with a tendency to feel less pain (median VAS 25 vs. 15 mm, p = 0.39) and being more satisfied (84.4% vs. 75.0%, p = 0.34).</p> <p>Conclusion</p> <p>Overall results do not demonstrate a benefit in using this pillow for lumbar punctures. This study results also suggest a benefit in the sub group of children over 6-year of age; this result needs confirmation.</p> <p>Trial Registration</p> <p>The trial was registered with Clinical Trials.gov (number NCT00775112).</p

Fil conducteur

Tronc d’un bouleau solitaire dans la région de Kuusamo (Finlande), en exposition multiple (2020), © Jonathan Lhoir.« Les technocrates, si on leur donnerait le Sahara, dans cinq ans faudrait qu’ils achètent du sable ailleurs. » Michel ColucciDans l’objectif général d’un ouvrage proposant un autre récit fondateur de la coopération territoriale, cette introduction ancre ce dernier dans l’histoire de chercheurs passionnés « passeurs de frontières ».Qui sommes-nous ? Un collectif de chercheurs d’..

Analyzing 2D gel images using a two-component empirical bayes model

<p>Abstract</p> <p>Background</p> <p>Two-dimensional polyacrylomide gel electrophoresis (2D gel, 2D PAGE, 2-DE) is a powerful tool for analyzing the proteome of a organism. Differential analysis of 2D gel images aims at finding proteins that change under different conditions, which leads to large-scale hypothesis testing as in microarray data analysis. Two-component empirical Bayes (EB) models have been widely discussed for large-scale hypothesis testing and applied in the context of genomic data. They have not been implemented for the differential analysis of 2D gel data. In the literature, the mixture and null densities of the test statistics are estimated separately. The estimation of the mixture density does not take into account assumptions about the null density. Thus, there is no guarantee that the estimated null component will be no greater than the mixture density as it should be.</p> <p>Results</p> <p>We present an implementation of a two-component EB model for the analysis of 2D gel images. In contrast to the published estimation method, we propose to estimate the mixture and null densities simultaneously using a constrained estimation approach, which relies on an iteratively re-weighted least-squares algorithm. The assumption about the null density is naturally taken into account in the estimation of the mixture density. This strategy is illustrated using a set of 2D gel images from a factorial experiment. The proposed approach is validated using a set of simulated gels.</p> <p>Conclusions</p> <p>The two-component EB model is a very useful for large-scale hypothesis testing. In proteomic analysis, the theoretical null density is often not appropriate. We demonstrate how to implement a two-component EB model for analyzing a set of 2D gel images. We show that it is necessary to estimate the mixture density and empirical null component simultaneously. The proposed constrained estimation method always yields valid estimates and more stable results. The proposed estimation approach proposed can be applied to other contexts where large-scale hypothesis testing occurs.</p

Merleau-Ponty and the Measuring Body

In recent years a growing number of scholars in science studies and related fields are developing new ontologies to displace entrenched dualisms. These efforts often go together with a renewed interest in the roles played by symbolisms and tools in knowledge and being. This article brings Maurice Merleau-Ponty into these conversations, positioning him as a precursor of today’s innovative recastings of technoscience. While Merleau-Ponty is often invoked in relation to his early work on the body and embodiment, this article focuses on his later work, where the investigation of perception is integrated with an ontological exploration. The resulting approach revolves around the highly original idea of the body as a standard of measurement. We further develop this idea by coining the term ‘the measuring body’, which to a greater extent than did Merleau-Ponty accentuates the relative autonomy of symbolisms and tools and their capacity to decentre the perceiving body

Characterization of Macrophages and Osteoclasts in the Osteosarcoma Tumor Microenvironment at Diagnosis: New Perspective for Osteosarcoma Treatment?

Biological and histopathological techniques identified osteoclasts and macrophages as targets of zoledronic acid (ZA), a therapeutic agent that was detrimental for patients in the French OS2006 trial. Conventional and multiplex immunohistochemistry of microenvironmental and OS cells were performed on biopsies of 124 OS2006 patients and 17 surgical (“OSNew”) biopsies respectively. CSF-1R (common osteoclast/macrophage progenitor) and TRAP (osteoclast activity) levels in serum of 108 patients were correlated to response to chemotherapy and to prognosis. TRAP levels at surgery and at the end of the protocol were significantly lower in ZA+ than ZA− patients (padj = 0.0011; 0.0132). For ZA+-patients, an increase in the CSF-1R level between diagnosis and surgery and a high TRAP level in the serum at biopsy were associated with a better response to chemotherapy (p = 0.0091; p = 0.0251). At diagnosis, high CD163+ was associated with good prognosis, while low TRAP activity was associated with better overall survival in ZA− patients only. Multiplex immunohistochemistry demonstrated remarkable bipotent CD68+/CD163+ macrophages, homogeneously distributed throughout OS regions, aside osteoclasts (CD68+/CD163−) mostly residing in osteolytic territories and osteoid-matrix-associated CD68−/CD163+ macrophages. We demonstrate that ZA not only acts on harmful osteoclasts but also on protective macrophages, and hypothesize that the bipotent CD68+/CD163+ macrophages might present novel therapeutic targets