Anti-MPER antibodies with heterogeneous neutralization capacity are detectable in most untreated HIV-1 infected individuals

Background The MPER region of the HIV-1 envelope glycoprotein gp41 is targeted by broadly neutralizing antibodies. However, the localization of this epitope in a hydrophobic environment seems to hamper the elicitation of these antibodies in HIV infected individuals. We have quantified and characterized anti-MPER antibodies by ELISA and by flow cytometry using a collection of mini gp41-derived proteins expressed on the surface of 293T cells. Longitudinal plasma samples from 35 HIV-1 infected individuals were assayed for MPER recognition and MPER-dependent neutralizing capacity using HIV-2 viruses engrafted with HIV-1 MPER sequences. Results Miniproteins devoid of the cysteine loop of gp41 exposed the MPER on 293T cell membrane. Anti-MPER antibodies were identified in most individuals and were stable when analyzed in longitudinal samples. The magnitude of the responses was strongly correlated with the global response to the HIV-1 envelope glycoprotein, suggesting no specific limitation for anti-MPER antibodies. Peptide mapping showed poor recognition of the C-terminal MPER moiety and a wide presence of antibodies against the 2F5 epitope. However, antibody titers failed to correlate with 2F5-blocking activity and, more importantly, with the specific neutralization of HIV-2 chimeric viruses bearing the HIV-1 MPER sequence; suggesting a strong functional heterogeneity in anti-MPER humoral responses. Conclusions Anti-MPER antibodies can be detected in the vast majority of HIV-1 infected individuals and are generated in the context of the global anti-Env response. However, the neutralizing capacity is heterogeneous suggesting that eliciting neutralizing anti-MPER antibodies by immunization might require refinement of immunogens to skip nonneutralizing responses.

Soil quality assessment through a multi-approach analysis in soils of abandoned terraced land in NE Spain

The abandonment of agricultural land in mountainous areas has been an outstanding problem along the last century and has captured the attention of scientists, technicians and administrations, for the dramatic consequences sometimes occurred due to soil instability, steep slopes, rainfall regimes and wildfires. Hidromorfological and pedological alterations causing exceptional floods and accelerated erosion processes has therefore been studied, identifying the cause in the loss of landscape heterogeneity. Through the disappearance of agricultural works and drainage maintenance, slope stability has resulted severely affected. The mechanization of agriculture has caused the displacement of vines, olives and corks trees cultivation in terraced areas along the Mediterranean catchment towards more economically suitable areas. On the one hand, land use and management changes have implicated sociological changes as well, transforming areas inhabited by agricultural communities into deserted areas where the colonization of disorganized spontaneous vegetation has buried a valuable rural patrimony. On the other hand, lacking of planning and management of the abandoned areas has produced badlands and infertile soils due to wildfire and high erosion rates strongly degrading the whole ecosystems. In other cases, after land abandonment a process of soil regeneration has been recorded. Investigations have been conducted in a part of NE Spain where extended areas of terraced soils previously cultivated have been abandoned in the last century. The selected environments were semi-abandoned vineyards, semi-abandoned olive groves, abandoned stands of cork trees, abandoned stands of pine trees, scrubland of Cistaceaea, scrubland of Ericaceaea, and pasture. The research work was focused on the study of most relevant physical, chemical and biological soil properties, as well as runoff and erosion under soils with different plant cover to establish the abandonment effect on soil quality, due to the peculiarity and vulnerability of these soils with a much reduced depth. The period of observation was carried out from autumn 2009 to autumn 2010. The sediment concentration of soil erosion under vines was recorded as 34.52 g/l while under pasture it was 4.66 g/l. In addition, the soil under vines showed the least amount of organic matter, which was 12 times lower than all other soil environments. The carbon dioxide (CO2) and total glomalin (TG) ratio to soil organic carbon (SOC) in this soil was 0.11 and 0.31 respectively. However, the soil under pasture contained a higher amount of organic matter and showed that the CO2 and TG ratio to SOC was 0.02 and 0.11 respectively indicating that the soil under pasture better preserves the soil carbon pool. A similar trend was found in the intermediate soils in the sequence of land use change and abandonment. Soil structural stability increased in the two soil fractions investigated (0.25-2.00 mm, 2.0-5.6 mm) especially in those soils that did not undergo periodical perturbations like wildfires. Soil quality indexes were obtained by using relevant physical and chemical soil parameters. Factor analysis carried out to study the relationship between all soil parameters allowed to related variables and environments and identify those areas that better contribute to soil quality towards others that may need more attention to avoid further degradation processes

Seismic characterization of heterogeneous sedimentary and fractured rocks based on Biot's theory of poroelasticity

Understanding and quantifying seismic energy dissipation, which manifests itself in terms of velocity dispersion and attenuation, in fluid-saturated porous rocks is of considerable interest, since it offers the perspective of extracting information with regard to the elastic and hydraulic rock properties. There is increasing evidence to suggest that wave-induced fluid flow, or simply WIFF, is the dominant underlying physical mechanism governing these phenomena throughout the seismic, sonic, and ultrasonic frequency ranges. This mechanism, which can prevail at the microscopic, mesoscopic, and macroscopic scale ranges, operates through viscous energy dissipation in response to fluid pressure gradients and inertial effects induced by the passing wavefield. In the first part of this thesis, we present an analysis of broad-band multi-frequency sonic log data from a borehole penetrating water-saturated unconsolidated glacio-fluvial sediments. An inherent complication arising in the interpretation of the observed P-wave attenuation and velocity dispersion is, however, that the relative importance of WIFF at the various scales is unknown and difficult to unravel. An important generic result of our work is that the levels of attenuation and velocity dispersion due to the presence of mesoscopic heterogeneities in water-saturated unconsolidated clastic sediments are expected to be largely negligible. Conversely, WIFF at the macroscopic scale allows for explaining most of the considered data while refinements provided by including WIFF at the microscopic scale in the analysis are locally meaningful. Using a Monte-Carlo-type inversion approach, we compare the capability of the different models describing WIFF at the macroscopic and microscopic scales with regard to their ability to constrain the dry frame elastic moduli and the permeability as well as their local probability distribution. In the second part of this thesis, we explore the issue of determining the size of a representative elementary volume (REV) arising in the numerical upscaling procedures of effective seismic velocity dispersion and attenuation of heterogeneous media. To this end, we focus on a set of idealized synthetic rock samples characterized by the presence of layers, fractures or patchy saturation in the mesocopic scale range. These scenarios are highly pertinent because they tend to be associated with very high levels of velocity dispersion and attenuation caused by WIFF in the mesoscopic scale range. The problem of determining the REV size for generic heterogeneous rocks is extremely complex and entirely unexplored in the given context. In this pilot study, we have therefore focused on periodic media, which assures the inherent self- similarity of the considered samples regardless of their size and thus simplifies the problem to a systematic analysis of the dependence of the REV size on the applied boundary conditions in the numerical simulations. Our results demonstrate that boundary condition effects are absent for layered media and negligible in the presence of patchy saturation, thus resulting in minimum REV sizes. Conversely, strong boundary condition effects arise in the presence of a periodic distribution of finite-length fractures, thus leading to large REV sizes. In the third part of the thesis, we propose a novel effective poroelastic model for periodic media characterized by mesoscopic layering, which accounts for WIFF at both the macroscopic and mesoscopic scales as well as for the anisotropy associated with the layering. Correspondingly, this model correctly predicts the existence of the fast and slow P-waves as well as quasi and pure S-waves for any direction of wave propagation as long as the corresponding wavelengths are much larger than the layer thicknesses. The primary motivation for this work is that, for formations of intermediate to high permeability, such as, for example, unconsolidated sediments, clean sandstones, or fractured rocks, these two WIFF mechanisms may prevail at similar frequencies. This scenario, which can be expected rather common, cannot be accounted for by existing models for layered porous media. Comparisons of analytical solutions of the P- and S-wave phase velocities and inverse quality factors for wave propagation perpendicular to the layering with those obtained from numerical simulations based on a ID finite-element solution of the poroelastic equations of motion show very good agreement as long as the assumption of long wavelengths remains valid. A limitation of the proposed model is its inability to account for inertial effects in mesoscopic WIFF when both WIFF mechanisms prevail at similar frequencies. Our results do, however, also indicate that the associated error is likely to be relatively small, as, even at frequencies at which both inertial and scattering effects are expected to be at play, the proposed model provides a solution that is remarkably close to its numerical benchmark. -- Comprendre et pouvoir quantifier la dissipation d'énergie sismique qui se traduit par la dispersion et l'atténuation des vitesses dans les roches poreuses et saturées en fluide est un intérêt primordial pour obtenir des informations à propos des propriétés élastique et hydraulique des roches en question. De plus en plus d'études montrent que le déplacement relatif du fluide par rapport au solide induit par le passage de l'onde (wave induced fluid flow en anglais, dont on gardera ici l'abréviation largement utilisée, WIFF), représente le principal mécanisme physique qui régit ces phénomènes, pour la gamme des fréquences sismiques, sonique et jusqu'à l'ultrasonique. Ce mécanisme, qui prédomine aux échelles microscopique, mésoscopique et macroscopique, est lié à la dissipation d'énergie visqueuse résultant des gradients de pression de fluide et des effets inertiels induits par le passage du champ d'onde. Dans la première partie de cette thèse, nous présentons une analyse de données de diagraphie acoustique à large bande et multifréquences, issues d'un forage réalisé dans des sédiments glaciaux-fluviaux, non-consolidés et saturés en eau. La difficulté inhérente à l'interprétation de l'atténuation et de la dispersion des vitesses des ondes P observées, est que l'importance des WIFF aux différentes échelles est inconnue et difficile à quantifier. Notre étude montre que l'on peut négliger le taux d'atténuation et de dispersion des vitesses dû à la présence d'hétérogénéités à l'échelle mésoscopique dans des sédiments clastiques, non- consolidés et saturés en eau. A l'inverse, les WIFF à l'échelle macroscopique expliquent la plupart des données, tandis que les précisions apportées par les WIFF à l'échelle microscopique sont localement significatives. En utilisant une méthode d'inversion du type Monte-Carlo, nous avons comparé, pour les deux modèles WIFF aux échelles macroscopique et microscopique, leur capacité à contraindre les modules élastiques de la matrice sèche et la perméabilité ainsi que leur distribution de probabilité locale. Dans une seconde partie de cette thèse, nous cherchons une solution pour déterminer la dimension d'un volume élémentaire représentatif (noté VER). Cette problématique se pose dans les procédures numériques de changement d'échelle pour déterminer l'atténuation effective et la dispersion effective de la vitesse sismique dans un milieu hétérogène. Pour ce faire, nous nous concentrons sur un ensemble d'échantillons de roches synthétiques idéalisés incluant des strates, des fissures, ou une saturation partielle à l'échelle mésoscopique. Ces scénarios sont hautement pertinents, car ils sont associés à un taux très élevé d'atténuation et de dispersion des vitesses causé par les WIFF à l'échelle mésoscopique. L'enjeu de déterminer la dimension d'un VER pour une roche hétérogène est très complexe et encore inexploré dans le contexte actuel. Dans cette étude-pilote, nous nous focalisons sur des milieux périodiques, qui assurent l'autosimilarité des échantillons considérés indépendamment de leur taille. Ainsi, nous simplifions le problème à une analyse systématique de la dépendance de la dimension des VER aux conditions aux limites appliquées. Nos résultats indiquent que les effets des conditions aux limites sont absents pour un milieu stratifié, et négligeables pour un milieu à saturation partielle : cela résultant à des dimensions petites des VER. Au contraire, de forts effets des conditions aux limites apparaissent dans les milieux présentant une distribution périodique de fissures de taille finie : cela conduisant à de grandes dimensions des VER. Dans la troisième partie de cette thèse, nous proposons un nouveau modèle poro- élastique effectif, pour les milieux périodiques caractérisés par une stratification mésoscopique, qui prendra en compte les WIFF à la fois aux échelles mésoscopique et macroscopique, ainsi que l'anisotropie associée à ces strates. Ce modèle prédit alors avec exactitude l'existence des ondes P rapides et lentes ainsi que les quasis et pures ondes S, pour toutes les directions de propagation de l'onde, tant que la longueur d'onde correspondante est bien plus grande que l'épaisseur de la strate. L'intérêt principal de ce travail est que, pour les formations à perméabilité moyenne à élevée, comme, par exemple, les sédiments non- consolidés, les grès ou encore les roches fissurées, ces deux mécanismes d'WIFF peuvent avoir lieu à des fréquences similaires. Or, ce scénario, qui est assez commun, n'est pas décrit par les modèles existants pour les milieux poreux stratifiés. Les comparaisons des solutions analytiques des vitesses des ondes P et S et de l'atténuation de la propagation des ondes perpendiculaires à la stratification, avec les solutions obtenues à partir de simulations numériques en éléments finis, fondées sur une solution obtenue en 1D des équations poro- élastiques, montrent un très bon accord, tant que l'hypothèse des grandes longueurs d'onde reste valable. Il y a cependant une limitation de ce modèle qui est liée à son incapacité à prendre en compte les effets inertiels dans les WIFF mésoscopiques quand les deux mécanismes d'WIFF prédominent à des fréquences similaires. Néanmoins, nos résultats montrent aussi que l'erreur associée est relativement faible, même à des fréquences à laquelle sont attendus les deux effets d'inertie et de diffusion, indiquant que le modèle proposé fournit une solution qui est remarquablement proche de sa référence numérique.

Detecting Heterogeneous Risk Attitudes with Mixed Gambles

We propose a task for eliciting attitudes toward risk that is close to real-world risky decisions which typically involve gains and losses. The task consists of accepting or rejecting gambles that provide a gain with probability p and a loss with probability 1−p . We employ finite mixture models to uncover heterogeneity in risk preferences and find that (i) behavior is heterogeneous, with one half of the subjects behaving as expected utility maximizers, (ii) for the others, reference-dependent models perform better than those where subjects derive utility from final outcomes, (iii) models with sign-dependent decision weights perform better than those without, and (iv) there is no evidence for loss aversion. The procedure is sufficiently simple so that it can be easily used in field or lab experiments where risk elicitation is not the main experiment.

Termoquímica na Unicamp: depoimento sobre uma jornada de 25 anos

This article describes the progress of a group of investigation on thermochemistry, which started in 1972. A homemade calorimeter was employed to provide quantitative support to the information on interative effect between lanthanide cations and halides or pseudohalides, in non-aqueous solvents, previously derived from conductometric titrations. However, the features of this instrument were not able to detect the thermal effects. Therefore, the great input to the group came from the acquisition of an LKB commercial apparatus, by the University in 1975. Considering the historical development of the coordination chemistry in Brazil, which was previously dedicated to strutural features of adducts, without focusing the energetic envolved in any coordinationcompound. Since starting the thermochemistry study, numerous masters and doctoral thesis covering more than a hundred adducts and a reasonable number of chelates, were presented systematizing data in order to understand the behavior of this kind of coordination compounds (C. Airoldi and A. P. Chagas, Coord. Chem. Rev. 1992, 119, 29). This knowledge enabled an extension of the study to include some heterogeneous systems formed by natural or synthetic materials like immobilized silica gel, lamellar phosphate, phosphonate or sulphate compounds, clays, polysaccharides, chrysotile, soils, etc. Many students are now engaged as staff members in Universities, Research Instituitions or other private institutions, developing many activities. Due to a multiplying effect on the formation of researchers, the group is now reaching the fourth generation.

Heterogeneous products and tests for an appropriate aggregation level considering different qualities: evidence from fresh hake at Barcelona’s wholesale market

[cat] Aquest estudi destaca la importància de considerar un nivell d’agregació adequat en els anàlisis de demanda, ja que treballar utilitzant un nivell d’agregació inadequat pot donar lloc a estimacions esbiaixades. Aquest fet es mostra a través de l’anàlisi de diferents productes de lluç fresc comercialitzats a Mercabarna, el mercat majorista de Barcelona. La literatura sobre la demanda de peix tracta al lluç com un únic producte i espècie. No obstant això, en el mercat espanyol, es comercialitzen molts peixos com a lluç, els quals mostren comportaments molt diferents (des de béns inferiors fins a béns de luxe). Els resultats obtinguts, en concordança amb les observacions empíriques, demostren que l’anàlisi s’ha de realitzar amb un major grau de detall que a nivell d’espècie. Això qüestiona els resultats d’anteriors estudis de demanda i la majoria de les bases de dades, on l’observació del nivell d’agregació adequat dels productes no es té en compte.

Heterogeneous products and tests for an appropriate aggregation level considering different qualities: evidence from fresh hake at Barcelona’s wholesale market

[cat] Aquest estudi destaca la importància de considerar un nivell d’agregació adequat en els anàlisis de demanda, ja que treballar utilitzant un nivell d’agregació inadequat pot donar lloc a estimacions esbiaixades. Aquest fet es mostra a través de l’anàlisi de diferents productes de lluç fresc comercialitzats a Mercabarna, el mercat majorista de Barcelona. La literatura sobre la demanda de peix tracta al lluç com un únic producte i espècie. No obstant això, en el mercat espanyol, es comercialitzen molts peixos com a lluç, els quals mostren comportaments molt diferents (des de béns inferiors fins a béns de luxe). Els resultats obtinguts, en concordança amb les observacions empíriques, demostren que l’anàlisi s’ha de realitzar amb un major grau de detall que a nivell d’espècie. Això qüestiona els resultats d’anteriors estudis de demanda i la majoria de les bases de dades, on l’observació del nivell d’agregació adequat dels productes no es té en compte.

Factors affecting Hg (II) adsorption in soils from the Rio Negro basin (Amazon)

Mercury (II) adsorption studies in top soils (top 10 cm) from the Rio Negro basin show this process depends strongly on some selected parameters of the aqueous phase in contact with the soils. Maximum adsorption occurred in the pH range 3.0-5.0 (>90%). Dissolved organic matter shows an inhibitory effect on the availability of Hg (II) to be adsorbed by the soils, whereas a higher chloride content of the solution resulted in a lower adsorption of Hg (II) at pH 5.0. Soils with higher organic matter content were less affected by changes in the salinity. An increase in the initial Hg (II) concentration increased the amount of Hg (II) adsorbed by the soil and decreased the time needed to reach equilibrium. A Freundlich isotherm provided a good model for Hg (II) adsorption in the two types of soil studied. The kinetics of Hg (II) adsorption on Amazonian soils showed to be very fast and followed pseudo-second order kinetics. An environmental implication of these results is discussed under the real scenario present in the Negro River basin, where acidic waters are in contact with a soil naturally rich in mercury.

Mercury in soils and sediments from gold mining liabilities in Southern Amazonia

The 1980-1990 Amazonian gold rush left an enormous liability that increasingly has been substituted by developing fish aquaculture. This work aimed at the identification of the mercury levels in the environment, associated with fish farms located in the North of Mato Grosso State, Southern Amazon. Sediment and soil samples were analyzed for total organic carbon and total mercury. Results indicate that the chemical characteristics of the sediment largely depend on the management procedures of the fish pond (liming, fish food used and fish population). The soils presented relatively low concentrations when compared with other data from the literature.

A screening method for detection of hexavalent chromium levels in soils

A rapid and low cost method to determine Cr(VI) in soils based upon alkaline metal extraction at room temperature is proposed as a semi-quantitative procedure to be performed in the field. A color comparison with standards with contents of Cr(VI) in the range of 10 to 150 mg kg-1 was used throughout. For the different types of soils studied, more than 75% of the fortified soluble Cr(VI) were recovered for all levels of spike tested for both the proposed and standard methods. Recoveries of 83 and 99% were obtained for the proposed and the standard methods, respectively, taking into account the analysis of a heavily contaminated soil sample.

Alkaline earth layered benzoates as reusable heterogeneous catalysts for the methyl esterification of benzoic acid

This paper describes the synthesis and characterization of layered barium, calcium and strontium benzoates and evaluates the potential of these materials as catalysts in the synthesis of methyl benzoate. The methyl esterification of benzoic acid was investigated, where the effects of temperature, alcohol:acid molar ratio and amount of catalyst were evaluated. Ester conversions of 65 to 70% were achieved for all the catalysts under the best reaction conditions. The possibility of recycling these metallic benzoates was also demonstrated, evidenced by unaltered catalytic activity for three consecutive reaction cycles.

Stratification of regional sampling by model-predicted changes of carbon stocks in Forested mineral soils

Selective papers of the workshop on "Development of models and forest soil surveys for monitoring of soil carbon", Koli, Finland, April 5-9 2006.

Carbon sequestration rates in Swedish forest soils : a comparison of three approaches

Selective papers of the workshop on "Development of models and forest soil surveys for monitoring of soil carbon", Koli, Finland, April 5-9 2006.