Miracle-dz/UniFAR-FTUs huggingface dataset:
Fidélité de la terminaison de la traduction chez les eucaryotes

La terminaison de la traduction se produit lorsqu’un codon stop entre au site A du ribosome ou il est reconnu par le facteur de terminaison eRF1 accompagne du facteur eRF3. Cette etape de la traduction est encore mal comprise chez les eucaryotes. Au cours de ma these je me suis interessee a l’etude de la fidelite de la terminaison de la traduction afin de mieux comprendre et caracteriser les mecanismes moleculaires mis en jeu lors du decodage du codon stop.L’un de mes projets consistait a mieux caracteriser une region du domaine N-terminal d’eRF1, la cavite P1, identifiee comme etant impliquee dans l’efficacite de terminaison. Grâce a une quantification de l’efficacite de translecture de mutants de la cavite P1, j’ai pu mettre en evidence le role de residus cles comme les serines 33 et 70, impliquees dans le decodage specifique du codon UGA probablement via une interaction directe entre les deux residus, ou encore l’arginine 65 et la lysine 109, essentielles pour une terminaison efficace sur les trois codons stop. L’analyse par RMN de ces mutants a egalement permis de montrer que ces residus etaient importants pour la conformation correcte de la cavite et potentiellement impliques dans une interaction directe avec l’ARNm. La combinaison des donnees genetiques et structurales nous a permis de proposer un modele d’interaction entre l’ARNm et le facteur de terminaison eRF1 dans lequel le codon stop serait reconnu en partie par l’intermediaire de la cavite P1. Dans la cellule, la terminaison est toujours en competition avec la translecture, qui correspond a l’incorporation d’un ARNt proche-cognat au niveau du codon stop. Afin d’identifier les acides amines incorpores par translecture au niveau du codon stop, j’ai mis au point un systeme base sur l’expression et la purification de proteines issues de la translecture qui sont ensuite analysees par spectrometrie de masse. J’ai pu mettre en evidence que la glutamine, la tyrosine et la lysine s’incorporent au niveau des codons UAA et UAG, alors que le tryptophane, la cysteine et l’arginine sont retrouves au niveau du codon UGA. J’ai egalement pu montrer que le contexte en 5’ n’influencait pas l’incorporation des acides amines au codon stop mais qu’en revanche, la presence de la paromomycine avait un impact sur la selection des ARNt suppresseurs naturels. Ce projet permet d’apporter de nouvelles informations sur les regles de decodage grâce a l’analyse des appariements entre codons stop et anticodons des ARNt naturels suppresseurs. Il permet egalement d’envisager des perspectives therapeutiques dans le cadre des maladies liees a la presence d’un codon stop premature et pour lesquelles le traitement repose sur l’utilisation de la translecture afin de re-exprimer des proteines entieres.
ATRAZINA: UN HERBICIDA POLÉMICO

The herbicide atrazine is being used for weed control in crops and also in nonagricultural areas. It is one of the most commonly used herbicides worldwide, presents variable biodegradation rates and has been detected in both surface water and groundwater systems. Because this herbicide is associated with relatively high chronic toxicity, accumulation potential and persistence in surface water and groundwater, the use of this herbicide has been restricted in the United States and prohibited in several countries of the European Community. In Mexico, the use of atrazine is not regulated and it is being widely used in agricultural areas. Since this herbicide has been detected in both surface water and groundwater and in concentrations higher than the recommended limits for drinking water, we have reviewed the mechanisms of natural attenuation of this herbicide, especially in agricultural areas, to decide upon the need for implementing regulation measures. Mexican water quality regulations provide limits for some pesticides but these do not include limits for atrazine. However, the use of atrazine in agricultural areas may represent a risk to contaminate water by transport of the herbicide or its degradation products to water bodies. To inquire about the need to regulate the use of atrazine in Mexico, this paper presents the results of natural attenuation of atrazine in Mexican agricultural areas, obtained through a research program carried out at the Mexican Institute of Water Technology (IMTA), with the support of graduate students from the Engineering and Earth Sciences Graduate Programs of the Mexican National Autonomous University (UNAM). In this paper we review the literature to provide information on the legal framework for uses of atrazine, the transport and natural attenuation mechanisms of the herbicide, the risks of contaminating water, and we discuss the necessity to restrict the use of this herbicide or to regulate concentrations in water and how farming practices should be modified to protect surface water and groundwater.
Single Ion Free Energies and Entropies of Aqueous Ions

Single ion free energies of hydration were assigned by Latimer, Pitzer, and Slansky by choosing a set of ion radii which made both negative and positive ions fall on the theoretical Born curve in a plot of ΔF against 1/r′. The r′ values were the crystal ion radii plus 0.1 A for negative ions and plus 0.85 A for positive ions. It is now shown that this assignment of single ion free energies is consistent with the single ion entropies of hydration if SH+ is —2.1 (the Eastman value). The ΔS values are proportional to Z/r′ and the tentative suggestion is made that it is the temperature coefficient of r′ which leads to the Z/r′ function. It is proposed that the ΔF values be used to calculate a consistent set of radii of aqueous ions which will take into account coordination numbers and polarization.
Determination of the hydrogen diffusion coefficient in hydrogenated amorphous silicon from hydrogen effusion experiments

The high‐temperature hydrogen evolution process from undoped hydrogenated amorphous silicon (a‐Si:H) is known to be diffusion limited. A formula is derived by which the hydrogen diffusion coefficient can be inferred from hydrogen effusion spectra taken at different heating rates or on films of different thickness. Experimental results for glow‐discharge a‐Si:H films prepared at various laboratories are presented and an excellent agreement to literature data of the hydrogen diffusion coefficient is obtained for undoped and phosphorus‐doped samples. For boron‐doped films, on the other hand, surface desorption of hydrogen from internal surfaces (voids) is found to be the rate‐limiting process for hydrogen evolution.
Effects of anaerobic digestion on digestate nutrient availability and crop growth: A review

Anaerobic digestion (AD) for biogas production leads to several changes in the composition of the resulting digestates compared to the original feedstock (ammonia content, pH, carbon to nitrogen ratio, etc.), which are relevant for the plant availability of macro‐ and micronutrients after field application. Increased NH4+‐N content in digested slurries compared to undigested slurries does not guarantee improved uptake efficiency of slurry nitrogen and increased savings in fertilizer nitrogen. AD of crop residues and cover crops leads to an increase in the total amounts of mobile organic manures within the farming system, resulting in a higher nitrogen use efficiency and an increased scope for target‐oriented nitrogen application in time and space, when needed by the crop, as an alternative to the site‐bound soil incorporation as green manures. AD of dairy manure appears to reduce the fraction of immediate plant available phosphorus and micronutrients. This does, however, not affect short‐term crop availability under field conditions. More studies are needed to improve current knowledge on sulfur losses during AD and fertilizer value of digestates.
Ab initio photoionization dynamics of β-alanine

Photoionization dynamics of β-alanine is studied by the trajectory simulations using the ab initio potential energy surface. Vertical photoionization in the spirit of the Franck-Condon principle is assumed both for the adiabatic and thermostatic simulations. Both intramolecular proton transfer and fragmentation while only the proton transfer are found in the thermostatic and adiabatic simulations, respectively, for the conformer having the intramolecular hydrogen bond N⋯H–O. The theoretical predictions are in line with the experimental observations available in the literatures. It is reported for the first time that the thermostatic temperatures strongly affect the fragmentation processes induced by photoionization.
Transparent conducting oxide semiconductors for transparent electrodes

The present status and prospects for further development of polycrystalline or amorphous transparent conducting oxide (TCO) semiconductors used for practical thin-film transparent electrode applications are presented in this paper. The important TCO semiconductors are impurity-doped ZnO, In2O3 and SnO2 as well as multicomponent oxides consisting of combinations of ZnO, In2O3 and SnO2, including some ternary compounds existing in their systems. Development of these and other TCO semiconductors is important because the expanding need for transparent electrodes for optoelectronic device applications is jeopardizing the availability of indium-tin-oxide (ITO), whose main constituent, indium, is a very expensive and scarce material. Al- and Ga-doped ZnO (AZO and GZO) semiconductors are promising as alternatives to ITO for thin-film transparent electrode applications. In particular, AZO thin films, with a low resistivity of the order of 10−5 Ω cm and source materials that are inexpensive and non-toxic, are the best candidates. However, further development of the deposition techniques, such as magnetron sputtering or vacuum arc plasma evaporation, as well as of the targets is required to enable the preparation of AZO and GZO films on large area substrates with a high deposition rate.
Approche des mécanismes de synthèse par carboréduction et de frittage « flash » de l’oxycarbure de zirconium :

Lors de ce travail, la synthese par carboreduction de la zircone a permis de synthetiser des poudres fines et de stoechiometrie variable d’oxycarbure de zirconium ZrCxOy. Une etude par microscopie electronique en transmission a permis d’identifier certains des mecanismes elementaires regissant la reaction de carboreduction de la zircone. Le developpement d’un modele numerique prenant en compte la densification d’un echantillon pulverulent d’oxycarbure a revele la presence de gradients thermiques et mecaniques dans l���echantillon. L’utilisation du frittage SPS (Spark Plasma Sintering) a rendu possible l’elaboration de monolithes de ZrCxOy denses, aux microstructures fines et homogenes permettant de conserver d’excellentes proprietes d’usage. L’etude des mecanismes elementaires gouvernant le fluage et le frittage a l’aide de modeles analytiques issus de lois de fluage a mis en evidence un role preponderant des dislocations dans le cas d’un traitement thermomecanique sous forte contrainte.
Extreme ultraviolet probing of laser ablation

This thesis details the use of extreme ultraviolet (EUV) sources in probing laser ablation and material opacity. The radiation hydrodynamic codes POLLUX and h2d are used to study the Rayleigh-Taylor instability in a regime relevant to inertial fusion energy and, in support of experimental effort, to test the feasibility of methods for measurement of iron opacity. Simulations of EUV radiography using the POLLUX code show how the presence of warm, dense material leads to strong absorption of the probe beam. Methods using both broad and narrowband EUV wavelength probes for benchmarking theoretical models of opacity are presented. An iron opacity experiment conducted at the Bhabha Atomic Research Centre is modelled, where K_alpha emission from an aluminium layer is used to probe an iron layer beneath. H2d simulations of laser heated iron, conducted to determine the suitability of experimental results obtained at the Rutherford Appleton Laboratory for iron opacity, show the difficulty in preventing large temperature and density gradients from forming. Interferometry has been used to measure both transmission and phase information for a 21.2 nm zinc EUV laser beam probing longitudinally through laser ablated CH plastic at the Prague Asterix Laser System. By conducting interferometric probing with EUV laser light, the region of warm dense matter between the critical surface and ablation surface in a laser ablated plasma is diagnosed. Analysis of phase shifts reveals refractive indices below solid and plasma values arising in CH plastic, due to bound-free absorption in C+, a model for which is presented. The transmission of the EUV probe beam provides a measure of the rate of ablation, matching previous experimental scaling laws.
Organic chemistry / Paula Yurkanis Bruice

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Involvement of Neuro-Immune Interactions in Pruritus With Special Focus on Receptor Expressions

Pruritus is a common, but very challenging symptom with a wide diversity of underlying causes like dermatological, systemic, neurological and psychiatric diseases. In dermatology, pruritus is the most frequent symptom both in its acute and chronic form (over 6 weeks in duration). Treatment of chronic pruritus often remains challenging. Affected patients who suffer from moderate to severe pruritus have a significantly reduced quality of life. The underlying physiology of pruritus is very complex, involving a diverse network of components in the skin including resident cells such as keratinocytes and sensory neurons as well as transiently infiltrating cells such as certain immune cells. Previous research has established that there is a significant crosstalk among the stratum corneum, nerve fibers and various immune cells, such as keratinocytes, T cells, basophils, eosinophils and mast cells. In this regard, interactions between receptors on cutaneous and spinal neurons or on different immune cells play an important role in the processing of signals which are important for the transmission of pruritus. In this review, we discuss the role of various receptors involved in pruritus and inflammation, such as TRPV1 and TRPA1, IL-31RA and OSMR, TSLPR, PAR-2, NK1R, H1R and H4R, MRGPRs as well as TrkA, with a focus on interaction between nerve fibers and different immune cells. Emerging evidence shows that neuro-immune interactions play a pivotal role in mediating pruritus-associated inflammatory skin diseases such as atopic dermatitis, psoriasis or chronic spontaneous urticaria. Targeting these bidirectional neuro-immune interactions and the involved pruritus-specific receptors is likely to contribute to novel insights into the underlying pathogenesis and targeted treatment options of pruritus.
Results of a Japanese ring study of a human Cell Line Activation Test (h-CLAT) for predicting skin sensitization potential (7^ Report) : A study for evaluating fragrance skin sensitization potential using h-CLAT

We are conducting a Japanese ring study to develop the human Cell Line Activation Test (h-CLAT). The aim of this study is to confirm whether the h-CLAT can predict skin sensitization for oxidative hair dyes. In addition, we studied the effect of test chemical fluorescence on prediction performance. h-CLATs were independently performed in two laboratories for eight chemicals, yielding good reproducibility between the laboratories. Good concordance was obtained between LLNA results and study chemicals. p-Phenylenediamine, which exhibits fluorescence at around 530 nm, which is in the h-CLAT measurement range, was correctly evaluated as positive by h-CLAT. It was possible to compensate for the influence of fluorescence in CD86/CD54 expression measurements, suggesting that substances exhiviting autofluorescence, such as oxidative hair dyes, can also be evaluated correctly. While a notably high, concentration-dependent CD54 expression was observed with Bandrowski’s base, this expression was not observed with p-phenylenediamine, a result which suggests that the sensitization responses of these two dyes may differ. In conclusion, it is suggested that h-CLAT is useful for evaluating the skin sensitization potential of oxidative hair dyes.
DNA-copolymers structure formation: beyond self-assembly

This thesis describes various synthetic strategies to generate DNA based amphiphilic copolymers which organized into functional structures. Scholar studies of the mechanism of structure formation were conducted considering the hydrophilic weight fraction as the key factor directing the self-assembly. Various modes of structure formation could be studied, inherent to that parameter i. e. , crystallization assisted self-assembly, emulsification and nucleation polymerization. The functionality of the resulting structures as well as their potential application were eventually assessed.
Nuclear Magnetic Resonance Spectroscopic and Computational Investigations of Chloroperoxidase Catalyzed Regio- and Enantio-Selective Transformations

OF THE DISSERTATION NUCLEAR MAGNETIC RESONANCE SPECTROSCOPIC AND COMPUTATIONAL INVESTIGATIONS OF CHLOROPEROXIDASE CATALYZED REGIOAND ENANTIO-SELECTIVE TRANSFORMATIONS by Rui Zhang Florida International University, 2013 Miami, Florida Professor Xiaotang Wang, Major Professor Chloroperoxidase (CPO) is the most versatile heme-containing enzyme that catalyzes a broad spectrum of reactions. The remarkable feature of this enzyme is the high regioand enantio-selectivity exhibited in CPO-catalyzed oxidation reactions. The aim of this dissertation is to elucidate the structural basis for regioand enantio-selective transformations and investigate the application of CPO in biodegradation of synthetic dyes. To unravel the mechanism of CPO-catalyzed regioselective oxidation of indole, the dissertation explored the structure of CPO-indole complex using paramagnetic relaxation and molecular modeling. The distances between protons of indole and the heme iron revealed that the pyrrole ring of indole is oriented toward the heme with its 2-H pointing directly at the heme iron. This provides the first experimental and theoretical explanation for the "unexpected" regioselectivity of CPO-catalyzed indole oxidation. Furthermore, the residues including Leu 70, Phe 103, Ile 179, Val 182, Glu 183, and Phe 186 were found essential to the substrate binding to CPO. These results will serve as a lighthouse in guiding the design of CPO mutants with tailor-made activities for biotechnological applications. To understand the origin of the enantioselectivity of CPO-catalyzed oxidation reactions, the interactions of CPO with substrates such as 2-(methylthio)thiophene were investigated by nuclear magnetic resonance spectroscopy (NMR) and computational techniques. In particular, the enantioselectivity is partly explained by the binding orientation of substrates.
Incorporating electric polarizabilities in water-water interaction potentials

Etude des potentiels d'interaction en incluant des corrections a n corps obtenues a partir des polarisabilites electriques classiques et des dipoles induits correspondants (modele a atomes polarisables). Application au calcul des structures cristallines et des energies reticulaires de glaces a protons ordonnes (phases II, IX et VIII)
Effects of local non‐equilibrium solute diffusion on rapid solidification of alloys

A conceptual foundation for the study of local non-equilibrium solute diffusion under rapid solidification conditions is proposed. The model takes into account the relaxation to local equilibrium of the solute flux and incorporates two diffusion speeds, V Db , the bulk liquid diffusion speed, and V Di , the interface diffusive speed, as the most important parameters governing the solute concentration in the liquid phase and solute partitioning. The analysis of the model predicts complete solute trapping and the transition to a purely thermally controlled solidification, which occur abruptly when the interface velocity V equals the bulk liquid diffusion speed V Db . The abrupt change in the solidification mechanism is described by the velocity dependent effective diffusion coefficient D * = D(1 - V 2 /V Db 2 ) and the generalized partition coefficient K * . If V > V Db , then D * = 0 and K * = 1. This implies an undisturbed diffusion field in the liquid (diffusionless solidification) and complete solute trapping at V > V Db . The interface diffusion speed V Di governs solute redistribution at a relatively low interface velocity V ∼ V Di < V Db . The influence of the local non-equilibrium solute transport on the temperature field and interface stability under rapid solidification conditions is also discussed.
A Miniature Quadrupole Mass Spectrometer Array and GC For Space Flight: Astronaut EVA and Cabin-Air Monitoring

A miniature quadrupole mass spectrometer array and g a s chromatograph have been designed and built for NASA flight missions. Without the gas chromatograph the mass spectrometer is to be u s e d for detection, by astronauts in EVA, of N2, 0 2 , the hydrazines, and NH3 leaks in the hull of the International Space Station, and of adsorbed hydrazines on the astronauts' suits. The fully-adapted astronaut system, with all software and visual readout, is c a l l e d the Trace Gas Analyzer. When interfaced with the miniature gas chromatographic system, the mass spectrometer w i l l be useful for a variety of NASA missions involving more complex gas mixtures. The missions include planetary exploration (to Venus, Europa, Titan, etc.), as w e l l as cabin-air monitoring for longduration human flight to the Moon, Mars, and beyond. A description of the miniature mass spectrometer, the Trace Gas Analyzer system and miniature g a s chromatograph front end is given, and test results a re shown for a variety of gas mixtures. A variety of possible flight applications is discussed.