Miracle-dz/UniFAR-FTUs huggingface dataset:
en vue de l'obtention du grade de Docteur de l'Université de Lyon - École normale supérieure de Lyon dans la spécialité Chimie préparée au Laboratoire de Chimie

We have shown previously that actomyosin contractility plays an important role in controlling nuclear movements in future interneurons born in the medial ganglionic eminence (MGE) [Bellion et al.: J Neurosci 2005; 25: 5691–5699]. Because microtubules are known to control the structural and motile properties of migrating neurons, we asked whether alterations in the dynamic instability of microtubules would impair MGE cell migration. Migration was analyzed in flat cocultures in which green-fluorescent-proteinexpressing MGE cells migrate on cortical cells from their explant of origin. A low (100 n M ) concentration of nocodazole shortened the leading process of MGE cells that nevertheless continued to migrate at the same rate but frequently changed their direction of migration relative to control cells. MGE cells treated with a higher (1 M ) concentration of nocodazole that strongly destabilized microtubules took on multipolar morphology. They extended thin and labile processes. MGE cells no longer exhibited directional migration and migration velocity slowed 2-fold. These results suggest that microtubule stability is crucial for Received: December 13, 2006 Accepted after revision: April 11, 2007 Christine Métin INSERM U839, Hôpital Pitié-Salpêtrière 47 Boulevard de l’Hôpital FR–75651 Paris Cédex 13 (France) Tel. +33 1 4216 2672, Fax +33 1 4570 9990, E-Mail metin@chups.jussieu. fr © 2008 S. Karger AG, Basel 0378–5866/08/0303–0132$24.50/0 Accessible online at: www.karger. com/dne te l-0 08 11 60 4, v er si on 1 10 A pr 2 01 3
Focal Points in Framed Strategic Forms

Only recently have attempts been made to formalize the idea of salience that underlies static focal points. Bacharach, Sugden, and Janssen formalize the players' descriptions of the strategies and, in many cases, derive focal points and salience in an intuitive way. However, these approaches apply to special classes of games only and leave some subtle kinds of salience unexplained. In order to overcome these limitations framed strategic forms together with a language invariance requirement on their solutions are proposed. Journal of Economic Literature Classification Number: C72.
Draft Genome Sequence of the Chronic, Nonclonal Cystic Fibrosis Isolate Pseudomonas aeruginosa Strain 18A

ABSTRACT Pseudomonas aeruginosa strain 18A is a clinical, nonclonal isolate retrieved from the sputum of a chronically infected cystic fibrosis patient. The genome of 18A was sequenced for comparison with environmental and clinical isolates to identify genes that might facilitate its persistence during infection.
Recherches en reconstruction 3D photométrique

La reconstruction de surfaces tridimensionnelles a partir de plusieurs cameras calibrees peut s'entrevoir sous plusieurs aspects, en particulier, sous des aspects geometriques ou photometriques. Les images contiennent un grand nombre d'informations dont la correspondance, l'ombrage et les contours. En reconstruction 3D multi-vues, toutes ces informations n'ont cependant ete que tres partiellement fusionnees. Pourtant en exploitant simultanement le maximum d'information disponible, nous devrions intuitivement obtenir de meilleurs resultats et des algorithmes plus robustes. Par ailleurs, nous avons aussi regulierement des connaissances a priori sur la scene ; connaissances qu'il est possible d'exploiter, par exemple en les inserant sous la forme de contraintes. Arriver a trouver un cadre rigoureux permettant de meler et exploiter naturellement et simultanement toutes ces informations pour les problemes de reconstruction 3D multi-vues serait donc particulierement pertinent. Pour avancer dans cet objectif, il est necessaire de se replonger et de travailler la modelisation. Dans ce manuscrit, je presente les travaux que j'ai menes dans ce domaine autour de toutes ces questions. Ce manuscrit est aussi l'occasion pour moi de presenter les objectifs et activites de l'equipe de recherche STEEP que je anime et coordonne depuis sa creation en 2010.
Improving relevance in search through Ontology and Query Expansion

Prof. Pushpak Bhattacharyya Computer Science and Engineering department Bachelor of Technology Improving relevance in search through Ontology and Query Expansion by Anirudh Vemula From the inception of Semantic Web in the late 20th century, ontology has been a major focus to achieve the idea of semantic search. In this work, we will review different approaches that have been employed over the years to bring this idea into realization. Ontology brings in domain-specific knowledge which the keyword-based approaches lack, thereby lacking the capability of semantic search. We will see how exploiting ontology improves performance of an information retrieval system, more so when the data is very domain-specific such as Medical databases and E-commerce data. The performance improvements through ontology have been exhibited through a prototype implementation which uses a simplistic approach and still achieves significant improvement, thus showing the capabilities of ontology-based IR. We will also look into query expansion which rose as a solution to the vocabulary problem but has now become an essential part of state-of-the-art information retrieval systems. An extensive survey of the literature in the area of query expansion paves the way for our future work to introduce ontology into the query expansion framework.
High resolution soft x-ray tomography in the Madison Symmetric Torus

We present in this article the description of the upgraded soft x-ray tomographic diagnostic which has been installed in the Madison symmetric torus (MST) reversed field pinch. The previous diagnostic has been extended with two manipulators, for a total of three moveable probes and a fixed one. The line integrated emissivity (brightness) will be measured with arrays of photodiodes and the total number of channels has been increased from 24 to 74. The electronic layout has also been upgraded, and a type of custom made current-to-voltage amplifier has been developed. The diagnostic will be used to continue and extend the magnetohydrodynamics analysis of the MST plasma. The imaging of rotating coherent structures (one or, as recently showed, two) which appear during quasisingle helicity or pulsed poloidal current drive experiments will be performed in more detail. The photocameras can be easily extracted, modified, and inserted again, allowing applications and utilizations of the diagnostic.
Mouse Paneth cell defensins: primary structures and antibacterial activities of numerous cryptdin isoforms

Cryptdins are antimicrobial peptides of the defensin family that are produced by intestinal Paneth cells. mRNAs encoding 17 cryptdin isoforms have been characterized from a cDNA library generated from a single jejunal crypt. Six cryptdin cDNAs correspond to known peptides, and the remainder predict 11 novel Paneth cell defensins. Most cryptdin cDNAs have > or = 93% nucleotide sequence identity overall, except for cryptdin 4 and 5 cDNAs, whose respective mature peptide-encoding regions are only 74 and 78% identical to that of cryptdin 1. Cryptdin cDNAs differ at a small number of nucleotide positions: frequent substitutions were found in codons 38 and 52 of the propiece and in codons 68, 73, 76, 87, and 89 of the deduced peptides; cDNA clones with changes in codons 74, 83, and 88 were found, but there were fewer of these. The antimicrobial activities of cryptdins 1 to 6 were tested against Escherichia coli ML35 in two assays. In an agar diffusion assay, the potencies of cryptdins 1 to 3, 5, and 6 were approximately equivalent to that of rabbit neutrophil defensin NP-1 but cryptdin 4 was 30 times more active than NP-1. In a bactericidal assay system, cryptdins 1 and 3 to 6 were equally active at 10 micrograms/ml but cryptdin 2 and rabbit NP-1 were not active at this concentration. Since cryptdins 2 and 3 differ only at residue 10 (Thr and Lys, respectively), this amino acid appears to function in bactericidal interaction with E. coli. The demonstration that Paneth cells express a diverse population of microbicidal defensins further implicates cryptdins in restricting colonization or invasion of small intestinal epithelium by bacteria.
Are Two-Part Tariffs Efficient When Consumers Plan Ahead?: An Empirical Study

During the last two decades there has been an increase in using dynamic tariffs for billing household electricity consumption. This has questioned the suitability of traditional pricing schemes, such as two-part tariffs, since they contribute to create marked peak and offpeak demands. The aim of this paper is to assess if two-part tariffs are an efficient pricing scheme using Spanish household electricity microdata. An ordered probit model with instrumental variables on the determinants of power level choice and non-paramentric spline regressions on the electricity price distribution will allow us to distinguish between the tariff structure choice and the simultaneous demand decisions. We conclude that electricity consumption and dwellings’ and individuals’ characteristics are key determinants of the fixed charge paid by Spanish households Finally, the results point to the inefficiency of the two-part tariff as those consumers who consume more electricity pay a lower price than the others.
Cloning and Identification of a Novel Human Gene PDLIM5, a Homolog of AD-associated Neuronal Thread Protein (AD7c-NTP)

A novel human gene cDNA was successfully cloned from the human fetal brain cDNA library constructed by our lab, and this gene was termed PDLIM5 after acquiring the agreement of HUGO. BLASTX searching revealed that the hypothetical protein is a homolog of AD-associated neuronal thread protein (AD7c-NTP), which is over-expressed in Alzheimer disease (AD) beginning early in the course of disease, and over-expression of the AD7c-NTP gene would cause neuritic sprouting and cell death. SMART analysis showed that both our predicted protein and AD7c-NTP comprise BCL domain (only contains BH1 and BH2 regions). RT-PCR experiment revealed that the expression level of PDLIM5 in brain, skeletal muscle, prostate, colon and leukocyte is obviously higher than that in other tissues.
Comment on "Quantum State Transfer Between Matter and Light"

Matsukevich and Kuzmich (1) describe an interesting experiment directed toward the realization of scalable quantum networks through the protocol of (2). In particular, they demonstrate coherence between two atomic ensembles comprising two cylindrical volumes of cold rubidium atoms within a single magnetooptical trap. The authors claim that their measurements “constitute a complete set of tools required to build an arbitrary large-scale quantum network” and assert that this advance is achieved by way of several essential steps involving quantum entanglement.
Identifying the optimum source of mesenchymal stem cells for use in knee surgery

Single sitting procedures where the mononuclear cell fraction is extracted from bone marrow and implanted directly into cartilage and bone defects are becoming more popular as novel treatments for cartilage defects which have, until now had few treatment options. This is on the basis that the mesenchymal stem cells (MSCs) contained within will repair the damaged tissue. This study sought to determine if the femur and tibia could provide equivalent amounts of mesenchymal stem cells, with equivalent viability and proliferative capacity, to that obtained from the gold standard of the pelvis in order to potentially reduce the morbidity associated with these procedures. Bone marrow was extracted from the pelvis, femur, and tibia of human subjects. The mononuclear cell fraction was extracted and cultured in the laboratory. Mesenchymal stem cell populations were assessed using a colony forming unit count. Viability was assessed using a PrestoBlue viability assay. Population doubling number was calculated between the end of passage 0 and passage three to determine the proliferative abilities of the different populations. Finally, the cell surface phenotype of the cells was determined by flow cytometry. The results showed that the pelvis was superior to the femur and tibia in terms of the number of stem cells isolated. There was no statistically significant difference in the phenotype of the cells isolated from different locations. This work shows that when undertaking single sitting procedures, the pelvis remains the optimum source for obtaining MSCs, despite the morbidity associated with bone marrow collection from the pelvis. © 2017 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 35:1868–1875, 2017.
Basic Fibroblast Growth Factor Exhibits Dual and Rapid Regulation of Cyclin D1 and p27KIP1 to Stimulate Proliferation of Rat Cerebral Cortical Precursors

While extracellular signals play a major role in brain neurogenesis, little is known about the cell cycle machinery underlying mitogen stimulation of precursor proliferation. Current models suggest that the D cyclins function as primary sensors of extracellular mitogens. Here we define the mechanisms by which basic fibroblast growth factor (bFGF) stimulates cortical precursors, with particular attention to the responses of cell cycle promitogenic and antimitogenic regulators. bFGF produced a 4-fold increase in DNA synthesis and a 3-fold rise in bromodeoxyuridine labeling, suggesting that the factor promotes the G1/S transition. There was also a 3-fold increase in cyclin-dependent kinase 2 (CDK2) kinase activity, which is critical for S phase entry. CDK2 activation was apparently cyclin E dependent, since only its protein and mRNA levels were elevated at 24 h, whereas CDK2, p27KIP1 and p57KIP2 levels were unaltered. Late G1 phase CDK2/cyclin E activity depends on early G1 D cyclin function. Indeed, cyclin D1, but not cyclin D3, was upregulated selectively at 8 h after bFGF treatment, a time when cyclin E was unchanged. The sequential activation of cyclin D1 and cyclin E supports the idea that cyclin E gene transcription is regulated by cyclin-D/CDK4/6-mediated pRb phosphorylation and subsequent E2F transcription factor release. However, in addition to increased D1 cyclin, we unexpectedly detected a 75% reduction in p27KIP1 protein at 8 h, suggesting that both pro- and antimitogenic regulators are targets of extracellular mitogens during brain development.
Describing the Structural Diversity within an RNA's Ensemble

RNA is usually classified as either structured or unstructured; however, neither category is adequate in describing the diversity of secondary structures expected in biological systems We describe this diversity within the ensemble of structures by using two different metrics: the average Shannon entropy and the ensemble defect. The average Shannon entropy is a measure of the structural diversity calculated from the base pair probability matrix. The ensemble defect, a tool in identifying optimal sequences for a given structure, is a measure of the average number of structural differences between a target structure and all the structures that make up the ensemble, scaled to the length of the sequence. In this paper, we show examples and discuss various uses of these metrics in both structured and unstructured RNA. By exploring how these two metrics describe RNA as an ensemble of different structures, as would be found in biological systems, it will push the field beyond the standard “structured” and “unstructured” categorization.
La saliencia aberrante como base para la sintomatología psicótica

En este trabajo se plantea un primer estudio donde se presenta un instrumento de medida acerca de la saliencia aberrante (Cicero et al. 2010), su adaptacion, y su validacion a una poblacion tanto general como clinica. Dado un proceso tan relevante como la saliencia aberrante en psicopatologia en general, como en el ambito de las psicosis en particular, dotar a la practica clinica de un instrumento fiable y valido puede tener la mayor aplicabilidad y utilidad clinica. Asimismo, se plantea un segundo estudio centrado en un modelo de mediacion de la saliencia aberrante y su relacion con el pensamiento referencial y la dimension desorganizada para explicar, al menos parcialmente, la sintomatologia psicotica. Desde un punto de vista conceptual, aproximarnos a la relacion entre variables relativas a los procesos psicoticos es un objetivo relevante en si mismo, ya que puede permitir el estudio desde la propension a las fases iniciales de los estados psicoticos (o la psicopatologia grave en general). Por ultimo, con estos estudios se procura contribuir, aunque sea modestamente, a conocer la configuracion de todas estas caracteristicas del funcionamiento alterado del ser humano para mejorar el tratamiento y la calidad de vida de quienes padecen este tipo de trastornos o alteraciones.
ALZHEIMER'S DISEASE AND FRONTOTEMPORAL DEMENTIA DIFFERENTIAL AUTOMATIC DIAGNOSIS BASED ON SPECT IMAGES

Alzheimer's disease (AD) and frontotemporal dementia (FTD) are the most frequent neurodegenerative cognitive disorders, but their differential diagnosis is difficult. The aim of this study is to evaluate an automatic method that returns the probability that a patient suffers from AD or FTD from the analysis of brain SPECT (single photon emission computed tomography) images. A set of 116 descriptors was calculated from the images of 173 patients. Its size was reduced to 8 (using PLS). A model based on LDA (linear discriminant analysis) was subsequently built. Validation was carried out by means of the leave-one-out protocol. 83% of patients was properly diagnosed. Performances favorably compared to those of experts (range is 65-73%). Since images were acquired in different hospitals, the impact of the medical center on the diagnosis of both the classifier and the physicians was investigated
Nanostructured lipid carriers system: Recent advances in drug delivery

Nanostructured lipid carrier (NLC) is second generation smarter drug carrier system having solid matrix at room temperature. This carrier system is made up of physiological, biodegradable and biocompatible lipid materials and surfactants and is accepted by regulatory authorities for application in different drug delivery systems. The availability of many products in the market in short span of time reveals the success story of this delivery system. Since the introduction of the first product, around 30 NLC preparations are commercially available. NLC exhibit superior advantages over other colloidal carriers viz., nanoemulsions, polymeric nanoparticles, liposomes, SLN etc. and thus, have been explored to more extent in pharmaceutical technology. The whole set of unique advantages such as enhanced drug loading capacity, prevention of drug expulsion, leads to more flexibility for modulation of drug release and makes NLC versatile delivery system for various routes of administration. The present review gives insights on the definitions and characterization of NLC as colloidal carriers including the production techniques and suitable formulations. This review paper also highlights the importance of NLC in pharmaceutical applications for the various routes of drug delivery viz., topical, oral, pulmonary, ocular and parenteral administration and its future perspective as a pharmaceutical carrier.
Chlamydial Plasmid-Encoded Virulence Factor Pgp3 Neutralizes the Antichlamydial Activity of Human Cathelicidin LL-37

ABSTRACT Chlamydia trachomatis infection in the lower genital tract can ascend to and cause pathologies in the upper genital tract, potentially leading to severe complications, such as tubal infertility. However, chlamydial organisms depleted of plasmid or deficient in the plasmid-encoded Pgp3 are attenuated in ascending infection and no longer are able to induce the upper genital tract pathologies, indicating a significant role of Pgp3 in chlamydial pathogenesis. We now report that C. trachomatis Pgp3 can neutralize the antichlamydial activity of human cathelicidin LL-37, a host antimicrobial peptide secreted by both genital tract epithelial cells and infiltrating neutrophils. Pgp3 bound to and formed stable complexes with LL-37. We further showed that the middle region of Pgp3 (Pgp3m) was responsible for both the binding to and neutralization of LL-37, suggesting that Pgp3m can be targeted for attenuating chlamydial pathogenicity or developed for blocking LL-37-involved non-genital-tract pathologies, such as rosacea and psoriasis. Thus, the current study has provided significant information for both understanding the mechanisms of chlamydial pathogenesis and developing novel therapeutic agents.
Extracellular matrix receptors, ECMRII and ECMRI, for collagen and fibronectin correspond to VLA‐2 and VLA‐3 in the VLA family of heterodimers

The Very Late Activation Antigen (VLA) proteins are a family of five related heterodimers, which also are part of the integrin superfamily of cell adhesion molecules. Except for the identification of VLA‐5 as a fibronectin receptor structure, the functions of the VLA proteins have remained unclarified. In this paper, immuno‐precipitation experiments with both anti‐α and anti‐β subunit antibodies showed that the previously identified cell adhesion receptor for collagen, extracellular matrix receptor II (ECMRII), is equivalent to VLA‐2. At the same time a previously described multispecific cell adhesion receptor for collagen, fibroncclin, and laminin (ECMRI) has been shown to be identical to VLA‐3. Although the mAb 12F1 and P1H5 both recognized VLA‐2 (ECMRII), they appeared to define distinct epitopes on the α2 subunit. On the other hand, the mAb PIB5 and J143 recognized the α3 subunit of VLA‐3 (ECMRI) at or near the same site. Consistent with the collagen receptor functions of VLA‐2 (ECMRII) and VLA‐3 (ECMRI), anti‐VLA β antiserum blocked cell attachment to collagen.
Sistema avanzado de prototipado rápido para control en exoesqueletos y dispositivos mecatrónicos

La necesidad de automatizar sistemas complejos da origen a la ingenieria de control. Utilizando el principio de realimentacion, se pretende conseguir que las variables de interes del sistema se acerquen a un comportamiento deseado. En un principio se utilizaron sistemas de control basados en logica combinacional mediante reles y electronica analogica para tratar magnitudes mas ala de la logica binaria, estos sistemas adolecian de una gran falta de fiabilidad. Con la aparicion del microprocesador, se abrieron las posibilidades del control digital. Con el paso de las decadas, la necesidad de controlar sistemas grandes y complejos en plazos de tiempo cada vez mas cortos, provoco la aparicion de lenguajes de programacion de muy alto nivel, basados en graficos, que fueron adaptados para su utilizacion en sistemas de control. Son los denominados hardwares de control de prototipado rapido, mas conocidos como Rapid Control Prototyping hardware (RCP). El objetivo de la presente tesis doctoral es proponer y hacer realidad una solucion alternativa al uso de RCP comerciales, sin menoscabo de la capacidad computacional y de entrada/salida. Igualando o superando la facilidad, capacidad de programacion e interfaces de intercambio de datos. De forma que se tenga un RCP totalmente compatible con las herramientas de desarrollo de mas alto nivel utilizadas en ingenieria por un coste tan extremadamente reducido que permita disponer del RCP en gran numero. Las contribuciones presentadas en esta tesis han sido probadas y optimizadas, por lo que se dispone de la plataforma RCP con actuacion en tiempo real. Se esta empleando en multitud de Trabajos Fin de Grado, Tesis de Master y Tesis Doctorales, no ya solo en esta escuela, tambien en escuelas extranjeras.