312 research outputs found
FiabilitĂ© et fidĂ©litĂ©Â : les logiques humaines et matĂ©rielles Ă lâĆuvre dans les agences dâarchitecture de Pierre Dufau (1908-1985)
Actif de la fin des annĂ©es 1930 jusquâaux annĂ©es 1980, Pierre Dufau (1908-1985) est, par lâimportance quantitative de sa production bĂątie, lâun des principaux acteurs de lâarchitecture française des Trente Glorieuses. SpĂ©cialisĂ© dans la rĂ©alisation dâimmeubles de bureaux, de bĂątiments civils et dâĂ©quipements, il fait Ă©galement Ćuvre dans le domaine de lâurbanisme en concevant le plan de reconstruction dâAmiens puis en Ă©tant, trente ans plus tard, responsable du plan dâamĂ©nagement du Nouveau CrĂ©teil. Cet article propose dâĂ©tudier la structuration de lâagence en une entreprise proposant des produits Ă ses clients, et de la mettre en parallĂšle avec sa construction historiographique, celle-ci ayant Ă©tĂ© alimentĂ©e tant par la critique journalistique et lâexpertise historienne que par Pierre Dufau lui-mĂȘme, Ă travers lâĂ©criture de ses mĂ©moires.Active from the late 1930s to the 1980s, Pierre Dufau (1908-1985) is one of the leading performers in the French architecture during the Trente Glorieusesperiod, due to the quantitative importance of his built production. Specialized in office buildings, public buildings and facilities, he was also involved in the field of urban planning by designing the reconstruction plan of the city of Amiens, and thirty years later by being responsible for the conception of the âNouveau CrĂ©teilâmasterplan, in Paris suburbs. This article proposes to study the structuring of the agency into a company offering products to its customers, and to draw a parallel with its historiographical construction, fed as much by journalistic criticism and historian expertise as by Pierre Dufau himself through the writing of his memoirs
Non-selective Refocusing Pulse Design in Parallel Transmission for Magnetic Resonance Imaging of the Human Brain at Ultra High Field
In Magnetic Resonance Imaging (MRI), the increase of the static magnetic field strength is used to provide in theory a higher signal-to-noise ratio, thereby improving the overall image quality. The purpose of ultra-high-field MRI is to achieve a spatial image resolution sufficiently high to be able to distinguish structures so fine that they are currently impossible to view in a non-invasive manner. However, at such static magnetic fields strengths, the wavelength of the electromagnetic waves sent to flip the water proton spins is of the same order of magnitude than the scanned object. Interference wave phenomena are then observed, which are caused by the radiofrequency (RF) field inhomogeneity within the object. These generate signal and/or contrast artifacts in MR images, making their exploitation difficult, if not impossible, in certain areas of the body. It is therefore crucial to provide solutions to mitigate the non-uniformity of the spins excitation. Failing this, these imaging systems with very high fields will not reach their full potential.For relevant high field clinical diagnosis, it is therefore necessary to create RF pulses homogenizing the excitation of all spins (here of the human brain), and optimized for each individual to be imaged. For this, an 8-channel parallel transmission system (pTX) was installed in our 7 Tesla scanner. While most clinical MRI systems only use a single transmission channel, the pTX extension allows to simultaneously playing various forms of RF pulses on all channels. The resulting sum of the interference must be optimized in order to reduce the non-uniformity typically seen.The objective of this thesis is to synthesize this type of tailored RF pulses, using parallel transmission. These pulses will have as an additional constraint the compliance with the international exposure limits for radiofrequency exposure, which induces a temperature rise in the tissue. In this sense, many electromagnetic and temperature simulations were carried out as an introduction of this thesis, in order to assess the relationship between the recommended RF exposure limits and the temperature rise actually predicted in tissues.This thesis focuses specifically on the design of all RF refocusing pulses used in non-selective MRI sequences based on the spin-echo. Initially, only one RF pulse was generated for a simple application: the reversal of spin dephasing in the transverse plane, as part of a classic spin echo sequence. In a second time, sequences with very long refocusing echo train applied to in vivo imaging are considered. In all cases, the mathematical operator acting on the magnetization, and not its final state as is done conventionally, is optimized. The gain in high field imaging is clearly visible, as the necessary mathematical operations (that is to say, the rotation of the spins) are performed with a much greater fidelity than with the methods of the state of the art. For this, the generation of RF pulses is combining a k-space-based spin excitation method, the kT-points, and an optimization algorithm, called Gradient Ascent Pulse Engineering (GRAPE), using optimal control.This design is relatively fast thanks to analytical calculations rather than finite difference methods. The inclusion of a large number of parameters requires the use of GPUs (Graphics Processing Units) to achieve computation times compatible with clinical examinations. This method of designing RF pulses has been experimentally validated successfully on the NeuroSpin 7 Tesla scanner, with a cohort of healthy volunteers. An imaging protocol was developed to assess the image quality improvement using these RF pulses compared to typically used non-optimized RF pulses. All methodological developments made during this thesis have contributed to improve the performance of ultra-high-field MRI in NeuroSpin, while increasing the number of MRI sequences compatible with parallel transmission.En Imagerie par RĂ©sonance MagnĂ©tique (IRM), lâaugmentation du champ magnĂ©tique statique permet en thĂ©orie de fournir un rapport signal sur bruit accru, amĂ©liorant la qualitĂ© des images. Lâobjectif de lâIRM Ă ultra haut champ est dâatteindre une rĂ©solution spatiale suffisamment haute pour pouvoir distinguer des structures si fines quâelles sont actuellement impossibles Ă visualiser de façon non-invasive. Cependant, Ă de telles valeurs de champs magnĂ©tiques, la longueur dâonde du rayonnement Ă©lectromagnĂ©tique envoyĂ© pour basculer les spins des protons de lâeau est du mĂȘme ordre de grandeur que lâobjet dont on souhaite faire lâimage. Des phĂ©nomĂšnes dâinterfĂ©rences sont observĂ©s, ce qui se traduit par lâinhomogĂ©nĂ©itĂ© de ce champ radiofrĂ©quence (RF) au sein de lâobjet. Ces interfĂ©rences engendrent des artefacts de signal et/ou de contraste dans les images IRM, et rendent ainsi leur exploitation dĂ©licate. Il est donc crucial de fournir des solutions pour attĂ©nuer la non-uniformitĂ© de lâexcitation des spins, Ă dĂ©faut de quoi de tels systĂšmes ne pourront atteindre leurs pleins potentiels. Pour obtenir des diagnostics pertinents Ă trĂšs haut champ, il est donc nĂ©cessaire de crĂ©er des impulsions RF homogĂ©nĂ©isant l'excitation de l'ensemble des spins (ici du cerveau humain), optimisĂ©es pour chaque individu. Pour cela, un systĂšme de transmission parallĂšle (pTX) Ă 8 canaux a Ă©tĂ© installĂ© au sein de notre imageur Ă 7 Tesla. Alors que la plupart des systĂšmes IRM cliniques nâutilisent quâun seul canal dâĂ©mission, lâextension pTX permet de jouer diffĂ©rentes formes dâimpulsions RF de concert. La somme rĂ©sultante de ces interfĂ©rences doit alors ĂȘtre optimisĂ©e pour attĂ©nuer la non-uniformitĂ© observĂ©e classiquement. Lâobjectif de cette thĂšse est donc de synthĂ©tiser ce type dâimpulsions, en utilisant la pTX. Ces impulsions auront pour contrainte supplĂ©mentaire le respect des limitations internationales concernant l'exposition Ă des champs radiofrĂ©quence, qui induit une hausse de tempĂ©rature dans les tissus. En ce sens, de nombreuses simulations Ă©lectromagnĂ©tiques et de tempĂ©ratures ont Ă©tĂ© rĂ©alisĂ©es en introduction de cette thĂšse, afin dâĂ©valuer la relation entre les seuils recommandĂ©s dâexposition RF et lâĂ©lĂ©vation de tempĂ©rature prĂ©dite dans les tissus. Cette thĂšse porte plus spĂ©cifiquement sur la conception de lâensemble des impulsions RF refocalisantes utilisĂ©es dans des sĂ©quences IRM non-sĂ©lectives, basĂ©es sur lâĂ©cho de spin. Dans un premier temps, seule une impulsion RF a Ă©tĂ© gĂ©nĂ©rĂ©e, pour une application simple : lâinversion du dĂ©phasage des spins dans le plan transverse. Dans un deuxiĂšme temps, sont considĂ©rĂ©es les sĂ©quences Ă long train dâĂ©chos de refocalisation appliquĂ©es Ă lâin vivo. Ici, lâopĂ©rateur mathĂ©matique agissant sur la magnĂ©tisation, et non pas son Ă©tat final comme il est fait classiquement, est optimisĂ©. Le gain en imagerie Ă trĂšs haut champ est clairement visible puisque les opĂ©rations mathĂ©matiques (la rotation des spins) voulues sont rĂ©alisĂ©es avec plus de fidĂ©litĂ© que dans le cadre des mĂ©thodes de lâĂ©tat de lâart. Pour cela, la gĂ©nĂ©ration de ces impulsions RF combine une mĂ©thode dâexcitation des spins avec navigation dans lâespace de Fourier, les kT-points, et un algorithme dâoptimisation, appelĂ© Gradient Ascent Pulse Engineering (GRAPE), utilisant le contrĂŽle optimal. Cette conception est rapide grĂące Ă des calculs analytiques plus directs que des mĂ©thodes de diffĂ©rences finies. La prise en compte dâun grand nombre de paramĂštres nĂ©cessite lâusage de GPUs (Graphics Processing Units) pour atteindre des temps de calcul compatibles avec un examen clinique. Cette mĂ©thode de conception dâimpulsions RF a Ă©tĂ© validĂ©e expĂ©rimentalement sur lâimageur 7 Tesla de NeuroSpin, sur une cohorte de volontaires sains
Recurrent structural RNA motifs, Isostericity Matrices and sequence alignments
The occurrences of two recurrent motifs in ribosomal RNA sequences, the Kink-turn and the C-loop, are examined in crystal structures and systematically compared with sequence alignments of rRNAs from the three kingdoms of life in order to identify the range of the structural and sequence variations. Isostericity Matrices are used to analyze structurally the sequence variations of the characteristic non-WatsonâCrick base pairs for each motif. We show that Isostericity Matrices for non-WatsonâCrick base pairs provide important tools for deriving the sequence signatures of recurrent motifs, for scoring and refining sequence alignments, and for determining whether motifs are conserved throughout evolution. The systematic use of Isostericity Matrices identifies the positions of the insertion or deletion of one or more nucleotides relative to the structurally characterized examples of motifs and, most importantly, specifies whether these changes result in new motifs. Thus, comparative analysis coupled with Isostericity Matrices allows one to produce and refine structural sequence alignments. The analysis, based on both sequence and structure, permits therefore the evaluation of the conservation of motifs across phylogeny and the derivation of rules of equivalence between structural motifs. The conservations observed in Isostericity Matrices form a predictive basis for identifying motifs in sequences
Minor changes largely restore catalytic activity of archaeal RNase P RNA from Methanothermobacter thermoautotrophicus
The increased protein proportion of archaeal and eukaryal ribonuclease (RNase) P holoenzymes parallels a vast decrease in the catalytic activity of their RNA subunits (P RNAs) alone. We show that a few mutations toward the bacterial P RNA consensus substantially activate the catalytic (C-) domain of archaeal P RNA from Methanothermobacter, in the absence and presence of the bacterial RNase P protein. Large increases in ribozyme activity required the cooperative effect of at least two structural alterations. The P1 helix of P RNA from Methanothermobacter was found to be extended, which increases ribozyme activity (ca 200-fold) and stabilizes the tertiary structure. Activity increases of mutated archaeal C-domain variants were more pronounced in the context of chimeric P RNAs carrying the bacterial specificity (S-) domain of Escherichia coli instead of the archaeal S-domain. This could be explained by the loss of the archaeal S-domain's capacity to support tight and productive substrate binding in the absence of protein cofactors. Our results demonstrate that the catalytic capacity of archaeal P RNAs is close to that of their bacterial counterparts, but is masked by minor changes in the C-domain and, particularly, by poor function of the archaeal S-domain in the absence of archaeal protein cofactors
Verification of phylogenetic predictions in vivo and the importance of the tetraloop motif in a catalytic RNA
Electromagnetic and RF pulse design simulation based optimization of an eight-channel loop array for 11.7T brain imaging
Purpose: Optimization of transmit array performance is crucial in
ultra-high-field MRI scanners such as 11.7T because of the increased RF losses
and RF nonuniformity. This work presents a new workflow to investigate and
minimize RF coil losses, and to choose the optimum coil configuration for
imaging.
Methods: An 8-channel transceiver loop-array was simulated to analyze its loss
mechanism at 499.415 MHz. A folded-end RF shield was developed to limit radiation loss and improve the B+
1 efficiency. The coil element length, and the shield
diameter and length were further optimized using electromagnetic (EM) simulations. The generated EM fields were used to perform RF pulse design (RFPD)
simulations under realistic constraints. The chosen coil design was constructed
to demonstrate performance equivalence in bench and scanner measurements.
Results: The use of conventional RF shields at 11.7T resulted in significantly
high radiation losses of 18.4%. Folding the ends of the RF shield combined with
optimizing the shield diameter and length increased the absorbed power in biological tissue and reduced the radiation loss to 2.4%. The peak B+
1 of the optimal
array was 42% more than the reference array. Phantom measurements validated
the numerical simulations with a close match of within 4% of the predicted B+
1 .
Conclusion: A workflow that combines EM and RFPD simulations to numerically optimize transmit arrays was developed. Results have been validated using
phantom measurements. Our findings demonstrate the need for optimizing
the RF shield in conjunction with array element design to achieve efficient
excitation at 11.7T
The Microbial Rosetta Stone Database: A compilation of global and emerging infectious microorganisms and bioterrorist threat agents
BACKGROUND: Thousands of different microorganisms affect the health, safety, and economic stability of populations. Many different medical and governmental organizations have created lists of the pathogenic microorganisms relevant to their missions; however, the nomenclature for biological agents on these lists and pathogens described in the literature is inexact. This ambiguity can be a significant block to effective communication among the diverse communities that must deal with epidemics or bioterrorist attacks. RESULTS: We have developed a database known as the Microbial Rosetta Stone. The database relates microorganism names, taxonomic classifications, diseases, specific detection and treatment protocols, and relevant literature. The database structure facilitates linkage to public genomic databases. This paper focuses on the information in the database for pathogens that impact global public health, emerging infectious organisms, and bioterrorist threat agents. CONCLUSION: The Microbial Rosetta Stone is available at . The database provides public access to up-to-date taxonomic classifications of organisms that cause human diseases, improves the consistency of nomenclature in disease reporting, and provides useful links between different public genomic and public health databases
Optimizing full 3D SPARKLING trajectories for high-resolution T2*-weighted Magnetic Resonance Imaging
International audienceThe Spreading Projection Algorithm for Rapid K-space samplING, or SPARKLING, is an optimization-driven method that has been recently introduced for accelerated 2D T2*-w MRI using compressed sensing. It has then been extended to address 3D imaging using either stacks of 2D sampling patterns or a local 3D strategy that optimizes a single sampling trajectory at a time. 2D SPARKLING actually performs variable density sampling (VDS) along a prescribed target density while maximizing sampling efficiency and meeting the gradient-based hardware constraints. However, 3D SPARKLING has remained limited in terms of acceleration factors along the third dimension if one wants to preserve a peaky point spread function (PSF) and thus good image quality.In this paper, in order to achieve higher acceleration factors in 3D imaging while preserving image quality, we propose a new efficient algorithm that performs optimization on full 3D SPARKLING. The proposed implementation based on fast multipole methods (FMM) allows us to design sampling patterns with up to 10^7 k-space samples, thus opening the door to 3D VDS. We compare multi-CPU and GPU implementations and demonstrate that the latter is optimal for 3D imaging in the high-resolution acquisition regime (600”m isotropic). Finally, we show that this novel optimization for full 3D SPARKLING outperforms stacking strategies or 3D twisted projection imaging through retrospective and prospective studies on NIST phantom and in vivo brain scans at 3 Tesla. Overall the proposed method allows for 2.5-3.75x shorter scan times compared to GRAPPA-4 parallel imaging acquisition at 3 Tesla without compromising image quality
Comparative Analysis of Ribonuclease P RNA of the Planctomycetes
The planctomycetes, order Planctomycetales, are a distinct phylum of domain Bacteria. Genes encoding the RNA portion of ribonuclease P (RNase P) of some planctomycete members were sequenced and compared with existing database planctomycete sequences. rnpB gene sequences encoding RNase P RNA were generated by a conserved primer PCR strategy for Planctomyces brasiliensis, Planctomyces limnophilus, Pirellula marina, Pirellula staleyi strain ATCC 35122, Isosphaera pallida, one other Isosphaera strain, Gemmata obscuriglobus and three other strains of the Gemmata group. These sequences were aligned against reference bacterial sequences and secondary structures of corresponding RNase P RNAs deduced by a comparative approach. P12 helices were found to be highly variable in length, as were helices P16.1 and P19, when present. RNase P RNA secondary structures of Gemmata isolates were found to have unusual features relative to other planctomycetes, including a long P9 helix and an insert in the P13 helix not found in any other member of domain Bacteria. These unique features are consistent with other unusual properties of this genus, distinguishing it from other bacteria. Phylogenetic analyses indicate that relationships between planctomycetes derived from RNase P RNA are consistent with 16S rRNA-based analyses
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