Lithium ion rechargeable batteries: State of the art and future needs of microscopic theoretical models and simulations

This review deals with the recent developments and present status of the theoretical models for the simulation of the performance of lithium ion batteries. Preceded by a description of the main materials used for each of the components of a battery -anode, cathode and separator- and how material characteristics affect battery performance, a description of the main theoretical models describing the operation and performance of a battery are presented. The influence of the most relevant parameters of the models, such as boundary conditions, geometry and material characteristics are discussed. Finally, suggestions for future work are proposed.

Algorithms and computational tools for metabolic flux analysis

PhD thesis in Biomedical Engineering

Forward Looking and Myopic Regional Computable General Equilibrium Models. How Significant is the Distinction?

We present a stylized intertemporal forward-looking model able that accommodates key regional economic features, an area where the literature is not well developed. The main difference, from the standard applications, is the role of saving and its implication for the balance of payments. Though maintaining dynamic forward-looking behaviour for agents, the rate of private saving is exogenously determined and so no neoclassical financial adjustment is needed. Also, we focus on the similarities and the differences between myopic and forward-looking models, highlighting the divergences among the main adjustment equations and the resulting simulation outcomes.

Anatomy of contaminated aquifers of an industrial site: insights from the stable isotope compositions of waters and dissolved inorganic carbon

The hydrogen and oxygen isotopes of water and the carbon isotope composition of dissolved inorganic carbon (DIC) from different aquifers at an industrial site, highly contaminated by organic pollutants representing residues of the former gas production, have been used as natural tracers to characterize the hydrologic system. On the basis of their stable isotope compositions as well as the seasonal variations, different groups of waters (precipitation, surface waters, groundwaters and mineral waters) as well as seasonably variable processes of mixing between these waters can clearly be distinguished. In addition, reservoir effects and infiltration rates can be estimated. In the northern part of the site an influence of uprising mineral waters within the Quaternary aquifers, presumably along a fault zone, can be recognized. Marginal infiltration from the Neckar River in the cast and surface water infiltration adjacent to a steep hill on the western edge of the site with an infiltration rate of about one month can also be resolved through the seasonal variation. Quaternary aquifers closer to the centre of the site show no seasonal variations, except for one borehole close to a former mill channel and another borehole adjacent to a rain water channel. Distinct carbon isotope compositions and concentrations of DIC for these different groups of waters reflect variable influence of different components of the natural carbon cycle: dissolution of marine carbonates in the mineral waters, biogenic, soil-derived CO2 in ground- and surface waters, as well as additional influence of atmospheric CO2 for the surface waters. Many Quaternary aquifer waters have, however, distinctly lower delta(13)C(DIC) values and higher DIC concentrations compared to those expected for natural waters. Given the location of contaminated groundwaters at this site but also in the industrially well-developed valley outside of this site, the most likely source for the low C-13(DIC) values is a biodegradation of anthropogenic organic substances, in particular the tar oils at the site.

Back to the future in Chagas disease: from animal models to patient cohort studies, progress in immunopathogenesis research

Despite the wealth of information generated by trans-disciplinary research in Chagas disease, knowledge about its multifaceted pathogenesis is still fragmented. Here we review the body of experimental studies in animal models supporting the concept that persistent infection by Trypanosoma cruzi is crucial for the development of chronic myocarditis. Complementing this review, we will make an effort to reconcile seemingly contradictory results concerning the immune profiles of chronic patients from Argentina and Brazil. Finally, we will review the results of molecular studies suggesting that parasite-induced inflammation and tissue damage is, at least in part, mediated by the activities of trans-sialidase, mucin-linked lipid anchors (TLR2 ligand) and cruzipain (a kinin-releasing cysteine protease). One hundred years after the discovery of Chagas disease, it is reassuring that basic and clinical research tends to converge, raising new perspectives for the treatment of chronic Chagas disease.

Homology modeling and metabolism prediction of human carboxylesterase-2 using docking analyses by GriDock: a parallelized tool based on AutoDock 4.0.

Metabolic problems lead to numerous failures during clinical trials, and much effort is now devoted to developing in silico models predicting metabolic stability and metabolites. Such models are well known for cytochromes P450 and some transferases, whereas less has been done to predict the activity of human hydrolases. The present study was undertaken to develop a computational approach able to predict the hydrolysis of novel esters by human carboxylesterase hCES2. The study involved first a homology modeling of the hCES2 protein based on the model of hCES1 since the two proteins share a high degree of homology (congruent with 73%). A set of 40 known substrates of hCES2 was taken from the literature; the ligands were docked in both their neutral and ionized forms using GriDock, a parallel tool based on the AutoDock4.0 engine which can perform efficient and easy virtual screening analyses of large molecular databases exploiting multi-core architectures. Useful statistical models (e.g., r (2) = 0.91 for substrates in their unprotonated state) were calculated by correlating experimental pK(m) values with distance between the carbon atom of the substrate's ester group and the hydroxy function of Ser228. Additional parameters in the equations accounted for hydrophobic and electrostatic interactions between substrates and contributing residues. The negatively charged residues in the hCES2 cavity explained the preference of the enzyme for neutral substrates and, more generally, suggested that ligands which interact too strongly by ionic bonds (e.g., ACE inhibitors) cannot be good CES2 substrates because they are trapped in the cavity in unproductive modes and behave as inhibitors. The effects of protonation on substrate recognition and the contrasting behavior of substrates and products were finally investigated by MD simulations of some CES2 complexes.

Constraints on the upper Permian to upper Triassic marine carbon isotope curve : case studies from the Tethys

Secular variations of the seawater carbon isotopic composition provide evidence for paleoceanographic and paleoclimatic changes and may serve for chemiostratigraphic correlations. The present study aimed to improve the current knowledge on the Upper Permian and Triassic segment of the Phanerozoic marine carbon isotope curve, whose Triassic part was poorly constrained by previous studies. Profiles of inorganic carbon isotopes are provided for sections from Himalaya (Salt Range, Kashmir, Spiti and Nepal), Oman and North Dobrogea (Romania) on the basis of whole-rock carbonate analysis. The data acquired, together with a literature compilation confirmed that most of the Upper Permian is characterized by high δ13C values (averaging +40/00) but failed to detect a positive excursion as suggested by recent compilations. In the light of these observations, the large drop in δ13C values associated with the end-Permian mass extinction appears to be driven by a sudden transfer of previously stocked 13C depleted carbon, rather than by the overturn of a Late Permian stratified ocean. The Triassic data-set outlines significant secular variations. The best documented is a carbon isotope positive excursion just across the Lower-Middle Triassic boundary, globally developed since it was detected in various paleogeographic settings. It is interpreted to reflect variations in surface ocean chemistry, possibly related to increased primary productivity, at times when the biotic recovery after the end-Permian mass-extinction began to accelerate significantly and when a sharp rise in seawater δ34S values occurred globally. Strontium isotope data obtained from well preserved biogenic phosphates allow a refinement of the Middle Triassic segment of the seawater strontium isotope curve and show a major inflexion point of the seawater strontium isotope curve also near the Lower Triassic - Middle Triassic boundary. These facts suggest that the transition from the Early to the Middle Triassic was a time of revolutionary global change which represented an important step in the evolution of Mesozoic marine environments. A tentative carbon isotope curve for the Upper Permian to Upper Triassic time interval is proposed. Its major features are: ? high but constant δ13C values during the Late Permian ? a sharp drop in δ13C values in the latest Permian ? subsequent recovery of δ13C values ? a short-lived positive excursion across the Early-Middle Triassic boundary ? a gradual rise in δ13C values starting in the Late Ladinian or in the Early Carnian It is foreseen that these fluctuations of the carbon isotope curve may serve as chronostratigraphic markers and further assist in the correlation of Permian and Triassic carbonate deposits.

Metabolic Flux and Compartmentation Analysis in the Brain In vivo.

Through significant developments and progresses in the last two decades, in vivo localized nuclear magnetic resonance spectroscopy (MRS) became a method of choice to probe brain metabolic pathways in a non-invasive way. Beside the measurement of the total concentration of more than 20 metabolites, (1)H MRS can be used to quantify the dynamics of substrate transport across the blood-brain barrier by varying the plasma substrate level. On the other hand, (13)C MRS with the infusion of (13)C-enriched substrates enables the characterization of brain oxidative metabolism and neurotransmission by incorporation of (13)C in the different carbon positions of amino acid neurotransmitters. The quantitative determination of the biochemical reactions involved in these processes requires the use of appropriate metabolic models, whose level of details is strongly related to the amount of data accessible with in vivo MRS. In the present work, we present the different steps involved in the elaboration of a mathematical model of a given brain metabolic process and its application to the experimental data in order to extract quantitative brain metabolic rates. We review the recent advances in the localized measurement of brain glucose transport and compartmentalized brain energy metabolism, and how these reveal mechanistic details on glial support to glutamatergic and GABAergic neurons.

Hierarchical management of carbon sources is regulated similarly by the CbrA/B systems in Pseudomonas aeruginosa and Pseudomonas putida.

The CbrA/B system in pseudomonads is involved in the utilization of carbon sources and carbon catabolite repression (CCR) through the activation of the small RNAs crcZ in Pseudomonas aeruginosa, and crcZ and crcY in Pseudomonas putida. Interestingly, previous works reported that the CbrA/B system activity in P. aeruginosa PAO1 and P. putida KT2442 responded differently to the presence of different carbon sources, thus raising the question of the exact nature of the signal(s) detected by CbrA. Here, we demonstrated that the CbrA/B/CrcZ(Y) signal transduction pathway is similarly activated in the two Pseudomonas species. We show that the CbrA sensor kinase is fully interchangeable between the two species and, moreover, responds similarly to the presence of different carbon sources. In addition, a metabolomics analysis supported the hypothesis that CCR responds to the internal energy status of the cell, as the internal carbon/nitrogen ratio seems to determine CCR and non-CCR conditions. The strong difference found in the 2-oxoglutarate/glutamine ratio between CCR and non-CCR conditions points to the close relationship between carbon and nitrogen availability, or the relationship between the CbrA/B and NtrB/C systems, suggesting that both regulatory systems sense the same sort or interrelated signal.

The three phases of the ensemble forecasting of niche models: geographic range and shifts in climatically suitable areas of Utetheisa ornatrix (Lepidoptera, Arctiidae)

Species' geographic ranges are usually considered as basic units in macroecology and biogeography, yet it is still difficult to measure them accurately for many reasons. About 20 years ago, researchers started using local data on species' occurrences to estimate broad scale ranges, thereby establishing the niche modeling approach. However, there are still many problems in model evaluation and application, and one of the solutions is to find a consensus solution among models derived from different mathematical and statistical models for niche modeling, climatic projections and variable combination, all of which are sources of uncertainty during niche modeling. In this paper, we discuss this approach of ensemble forecasting and propose that it can be divided into three phases with increasing levels of complexity. Phase I is the simple combination of maps to achieve a consensual and hopefully conservative solution. In Phase II, differences among the maps used are described by multivariate analyses, and Phase III consists of the quantitative evaluation of the relative magnitude of uncertainties from different sources and their mapping. To illustrate these developments, we analyzed the occurrence data of the tiger moth, Utetheisa ornatrix (Lepidoptera, Arctiidae), a Neotropical moth species, and modeled its geographic range in current and future climates.

Multiple filtering devices for the estimation of cyclical DSGE models

We propose a method to estimate time invariant cyclical DSGE models using the informationprovided by a variety of filters. We treat data filtered with alternative procedures as contaminated proxies of the relevant model-based quantities and estimate structural and non-structuralparameters jointly using a signal extraction approach. We employ simulated data to illustratethe properties of the procedure and compare our conclusions with those obtained when just onefilter is used. We revisit the role of money in the transmission of monetary business cycles.

Trophic dynamics in the northern Humboldt Current system: insights from stable isotopes and stomach content analyses

The northern Humboldt Current system (NHCS) off Peru is one of the most productive world marine regions. It represents less than 0.1% of the world ocean surface but presently sustains about 10% of the world fish catch, with the Peruvian anchovy or anchoveta Engraulis ringens as emblematic fish resource. Compared with other eastern boundary upwelling systems, the higher fish productivity of the NHCS cannot be explained by a corresponding higher primary productivity. On another hand, the NHCS is the region where El Niño, and climate variability in general, is most notable. Also, surface oxygenated waters overlie an intense and extremely shallow Oxygen Minimum Zone (OMZ). In this context, the main objective of this study is to better understand the trophic flows in the NHCS using both stomach content and stable isotope analyses. The study focuses on a variety of organisms from low trophic levels such as zooplankton to top predators (seabirds and fur seals). The approach combines both long-term and specific studies on emblematic species such as anchoveta, and sardine Sardinops sagax and a more inclusive analysis considering the 'global' food web in the recent years (2008 – 2012) using stable isotope analysis. Revisiting anchovy and sardine we show that whereas phytoplankton largely dominated anchoveta and sardine diets in terms of numerical abundance, the carbon content of prey items indicated that zooplankton was by far the most important dietary component. Indeed for anchovy euphausiids contributed 67.5% of dietary carbon, followed by copepods (26.3%). Selecting the largest prey, the euphausiids, provide an energetic advantage for anchoveta in its ecosystem where oxygen depletion imposes strong metabolic constrain to pelagic fish. Sardine feed on smaller zooplankton than do anchoveta, with sardine diet consisting of smaller copepods and fewer euphausiids than anchoveta diet. Hence, trophic competition between sardine and anchovy in the northern Humboldt Current system is minimized by their partitioning of the zooplankton food resource based on prey size, as has been reported in other systems. These results suggest an ecological role for pelagic fish that challenges previous understanding of their position in the foodweb (zooplanktophagous instead of phytophagous), the functioning and the trophic models of the NHCS. Finally to obtain a more comprehensive vision of the relative trophic position of NHCS main components we used stable isotope analyses. For that purpose we analyzed the δ13C and δ15N stable isotope values of thirteen taxonomic categories collected off Peru from 2008 - 2011, i.e., zooplankton, fish, squids and air-breathing top predators. The δ15N isotope signature was strongly impacted by the species, the body length and the latitude. Along the Peruvian coast, the OMZ get more intense and shallow south of ~7.5ºS impacting the baseline nitrogen stable isotopes. Employing a linear mixed-effects modelling approach taking into account the latitudinal and body length effects, we provide a new vision of the relative trophic position of key ecosystem components. Also we confirm stomach content-based results on anchoveta Engraulis ringens and highlight the potential remarkable importance of an often neglected ecosystem component, the squat lobster Pleuroncodes monodon. Indeed, our results support the hypothesis according to which this species forage to some extent on fish eggs and larvae and can thus predate on the first life stages of exploited species. However, the δ13C values of these two species suggest that anchoveta and squat lobster do not exactly share the same habitat. This would potentially reduce some direct competition and/or predation.

The CbrA-CbrB two-component regulatory system controls the utilization of multiple carbon and nitrogen sources in Pseudomonas aeruginosa.

A novel two-component system, CbrA-CbrB, was discovered in Pseudomonas aeruginosa; cbrA and cbrB mutants of strain PAO were found to be unable to use several amino acids (such as arginine, histidine and proline), polyamines and agmatine as sole carbon and nitrogen sources. These mutants were also unable to use, or used poorly, many other carbon sources, including mannitol, glucose, pyruvate and citrate. A 7 kb EcoRI fragment carrying the cbrA and cbrB genes was cloned and sequenced. The cbrA and cbrB genes encode a sensor/histidine kinase (Mr 108 379, 983 residues) and a cognate response regulator (Mr 52 254, 478 residues) respectively. The amino-terminal half (490 residues) of CbrA appears to be a sensor membrane domain, as predicted by 12 possible transmembrane helices, whereas the carboxy-terminal part shares homology with the histidine kinases of the NtrB family. The CbrB response regulator shows similarity to the NtrC family members. Complementation and primer extension experiments indicated that cbrA and cbrB are transcribed from separate promoters. In cbrA or cbrB mutants, as well as in the allelic argR9901 and argR9902 mutants, the aot-argR operon was not induced by arginine, indicating an essential role for this two-component system in the expression of the ArgR-dependent catabolic pathways, including the aruCFGDB operon specifying the major aerobic arginine catabolic pathway. The histidine catabolic enzyme histidase was not expressed in cbrAB mutants, even in the presence of histidine. In contrast, proline dehydrogenase, responsible for proline utilization (Pru), was expressed in a cbrB mutant at a level comparable with that of the wild-type strain. When succinate or other C4-dicarboxylates were added to proline medium at 1 mM, the cbrB mutant was restored to a Pru+ phenotype. Such a succinate-dependent Pru+ property was almost abolished by 20 mM ammonia. In conclusion, the CbrA-CbrB system controls the expression of several catabolic pathways and, perhaps together with the NtrB-NtrC system, appears to ensure the intracellular carbon: nitrogen balance in P. aeruginosa.

Geochronological constraints on post-extinction recovery of the ammonoids and carbon cycle perturbations during the Early Jurassic

This paper presents the first quantitative study of the Early Jurassic recovery of ammonoids after the end-Triassic mass extinction based on detailed U-Pb ID-TIMS (isotope dilution thermal ionization mass spectrometry) geochronology from ash bed zircons placed within a clear phylogenetical and biochronological framework at the subzonal and species level. This study was triggered by the discovery of a rich Peruvian succession of ammonites, deposited concomitantly with an unusually large number of ash beds. Two major phases of rediversification are observed during the Psiloceras spelae and Angulaticeras zones that correspond to positive peaks in the delta C-13(org) curve, providing a possible link between biodiversity and the global carbon cycle. In the case of the post-extinction recovery, the development of the earliest Hettangian ammonites occurs within the genus Psiloceras, which begins with the occurrence of P. spelae and then explodes into worldwide development of smooth psiloceratids of the Psiloceras planorbis group s.l. This rapid biodiversification likely occurred less than 100 ka after the end-Triassic crisis; the genus Psiloceras occupied all the possible ecological niches worldwide, from the Pacific deep waters to the NW European shallow deposits and also in some rare Tethyan occurrences like at Germig in Tibet. This global dispersion allowed the differentiation of the group in several major phyla, the Schlotheimiidae, Discamphiceratinae, Arietitidae and Lytocerataceae, which were the roots of all other Jurassic and Cretaceous ammonites. (C) 2012 Elsevier B.V. All rights reserved.

Selecting statistical models to study the relationship between soybean yield and soil physical properties

Statistical models allow the representation of data sets and the estimation and/or prediction of the behavior of a given variable through its interaction with the other variables involved in a phenomenon. Among other different statistical models, are the autoregressive state-space models (ARSS) and the linear regression models (LR), which allow the quantification of the relationships among soil-plant-atmosphere system variables. To compare the quality of the ARSS and LR models for the modeling of the relationships between soybean yield and soil physical properties, Akaike's Information Criterion, which provides a coefficient for the selection of the best model, was used in this study. The data sets were sampled in a Rhodic Acrudox soil, along a spatial transect with 84 points spaced 3 m apart. At each sampling point, soybean samples were collected for yield quantification. At the same site, soil penetration resistance was also measured and soil samples were collected to measure soil bulk density in the 0-0.10 m and 0.10-0.20 m layers. Results showed autocorrelation and a cross correlation structure of soybean yield and soil penetration resistance data. Soil bulk density data, however, were only autocorrelated in the 0-0.10 m layer and not cross correlated with soybean yield. The results showed the higher efficiency of the autoregressive space-state models in relation to the equivalent simple and multiple linear regression models using Akaike's Information Criterion. The resulting values were comparatively lower than the values obtained by the regression models, for all combinations of explanatory variables.