Gene Expression Complex Networks: Synthesis, Identification, and Analysis

Thanks to recent advances in molecular biology, allied to an ever increasing amount of experimental data, the functional state of thousands of genes can now be extracted simultaneously by using methods such as cDNA microarrays and RNA-Seq. Particularly important related investigations are the modeling and identification of gene regulatory networks from expression data sets. Such a knowledge is fundamental for many applications, such as disease treatment, therapeutic intervention strategies and drugs design, as well as for planning high-throughput new experiments. Methods have been developed for gene networks modeling and identification from expression profiles. However, an important open problem regards how to validate such approaches and its results. This work presents an objective approach for validation of gene network modeling and identification which comprises the following three main aspects: (1) Artificial Gene Networks (AGNs) model generation through theoretical models of complex networks, which is used to simulate temporal expression data; (2) a computational method for gene network identification from the simulated data, which is founded on a feature selection approach where a target gene is fixed and the expression profile is observed for all other genes in order to identify a relevant subset of predictors; and (3) validation of the identified AGN-based network through comparison with the original network. The proposed framework allows several types of AGNs to be generated and used in order to simulate temporal expression data. The results of the network identification method can then be compared to the original network in order to estimate its properties and accuracy. Some of the most important theoretical models of complex networks have been assessed: the uniformly-random Erdos-Renyi (ER), the small-world Watts-Strogatz (WS), the scale-free Barabasi-Albert (BA), and geographical networks (GG). The experimental results indicate that the inference method was sensitive to average degree k variation, decreasing its network recovery rate with the increase of k. The signal size was important for the inference method to get better accuracy in the network identification rate, presenting very good results with small expression profiles. However, the adopted inference method was not sensible to recognize distinct structures of interaction among genes, presenting a similar behavior when applied to different network topologies. In summary, the proposed framework, though simple, was adequate for the validation of the inferred networks by identifying some properties of the evaluated method, which can be extended to other inference methods.

Full-dimensional analytical ab initio potential energy surface of the ground state of HOI

Extensive ab initio calculations using a complete active space second-order perturbation theory wavefunction, including scalar and spin-orbit relativistic effects with a quadruple-zeta quality basis set were used to construct an analytical potential energy surface (PES) of the ground state of the [H, O, I] system. A total of 5344 points were fit to a three-dimensional function of the internuclear distances, with a global root-mean-square error of 1.26 kcal mol(-1). The resulting PES describes accurately the main features of this system: the HOI and HIO isomers, the transition state between them, and all dissociation asymptotes. After a small adjustment, using a scaling factor on the internal coordinates of HOI, the frequencies calculated in this work agree with the experimental data available within 10 cm(-1). (C) 2011 American Institute of Physics. [doi: 10.1063/1.3615545]

Intermolecular vibrations and fast relaxations in supercooled ionic liquids

Short-time dynamics of ionic liquids has been investigated by low-frequency Raman spectroscopy (4 < omega < 100 cm(-1)) within the supercooled liquid range. Raman spectra are reported for ionic liquids with the same anion, bis(trifluoromethylsulfonyl)imide, and different cations: 1-butyl-3-methylimidazolium, 1-hexyl-3-methylimidazolium, 1-butyl-1-methylpiperidinium, trimethylbutylammonium, and tributylmethylammonium. It is shown that low-frequency Raman spectroscopy provides similar results as optical Kerr effect (OKE) spectroscopy, which has been used to study intermolecular vibrations in ionic liquids. The comparison of ionic liquids containing aromatic and non-aromatic cations identifies the characteristic feature in Raman spectra usually assigned to librational motion of the imidazolium ring. The strength of the fast relaxations (quasi-elastic scattering, QES) and the intermolecular vibrational contribution (boson peak) of ionic liquids with non-aromatic cations are significantly lower than imidazolium ionic liquids. A correlation length assigned to the boson peak vibrations was estimated from the frequency of the maximum of the boson peak and experimental data of sound velocity. The correlation length related to the boson peak (similar to 19 angstrom) does not change with the length of the alkyl chain in imidazolium cations, in contrast to the position of the first-sharp diffraction peak observed in neutron and X-ray scattering measurements of ionic liquids. The rate of change of the QES intensity in the supercooled liquid range is compared with data of excess entropy, free volume, and mean-squared displacement recently reported for ionic liquids. The temperature dependence of the QES intensity in ionic liquids illustrates relationships between short-time dynamics and long-time structural relaxation that have been proposed for glass-forming liquids. (C) 2011 American Institute of Physics. [doi: 10.1063/1.3604533]

Nickel sorption capacity of ground xylem of Quercus ilex trees and effects of selected ligands present in the xylem sap

In this work the influence of four different ligands present in the xylem sap of Quercus ilex (histidine, citric, oxalic and aspartic acids) on Ni(II) adsorption by xylem was investigated. Grinded xylem was trapped in acrylic columns and solutions of Ni(II), in the absence and presence of the four ligands prepared in KNO(3) 0-1 mol L(-1) at pH 5.5, were percolated through the column. Aliquots of solutions were recovered in the column end for Ni determination by graphite furnace atomic absorption spectrometry (GFAAS). The experimental. data to describe Ni sorption by xylem in both the presence and absence of ligands was better explained by the Freundlich isotherm model. The decreasing affinity order of ligands for Ni was: oxalic acid > citric acid > histidine > aspartic acid. On the other hand, the Ni(II) adsorption by xylem increased following the inverse sequence of ligands. Potentiometric titrations of acidic groups were carried out to elucidate the sorption site groups available in Q. ilex xylem. The potentiometric titration has shown three sorption sites: pK(a) 2.6 (57.7% of the sorption sites), related to monobasic aliphatic carboxylic acids or nitrogen aromatic bases, pK(a) 8.1 (9.6%) and pK(a) 9.9 (32.7%), related to phenolic groups. (C) 2008 Elsevier GmbH. All rights reserved.

Coconut coir as biosorbent for Cr(VI) removal from laboratory wastewater

A high cost-effective treatment of sulphochromic waste is proposed employing a raw coconut coir as biosorbent for Cr(VI) removal. The ideal pH and sorption kinetic, sorption capacities, and sorption sites were the studied biosorbent parameters. After testing five different isotherm models with standard solutions, Redlich-Peterson and Toth best fitted the experimental data, obtaining a theoretical Cr(VI) sorption capacity (SC) of 6.3 mg g(-1). Acid-base potentiometric titration indicated around of 73% of sorption sites were from phenolic compounds, probably lignin. Differences between sorption sites in the coconut coir before and after Cr adsorption identified from Fourier transform infrared spectra suggested a modification of sorption sites after sulphochromic waste treatment, indicating that the sorption mechanism involves organic matter oxidation and chromium uptake. For sulphocromic waste treatment, the SC was improved to 26.8 +/- 0.2 mg g(-1), and no adsorbed Cr(VI) was reduced, remaining only Cr(III) in the final solution. The adsorbed material was calcinated to obtain Cr2O3, with a reduction of more than 60% of the original mass. (c) 2008 Elsevier B.V. All rights reserved.

ECAP of Fe. Experiments and simulations of the in-elbow textures

The study of deformation properties of low carbon steels is of particular interest because of their many technological applications. Obtaining fine grained Fe based materials can be approached by one of the several available Severe Plastic Deformation (SPD) techniques. The current paper shows experimental data and simulations of the deformation process of iron samples by Equal Channel Angular Extrusion (ECAE). The samples were extruded in a 120 degrees channel die either by one or a few passes. The heterogeneity and local development of the deformation on the elbow of the channel has been studied by X-ray measuring and simulation of the texture evolution. The Self Consistent models used for simulation allowed the calculation of the spin of the main texture components which agreed pretty well with the experiments.

Clarification of a wheat straw-derived medium with ion-exchange resins for xylitol crystallization

BACKGROUND: Xylitol bioproduction from lignocellulosic residues comprises hydrolysis of the hemicellulose, detoxification of the hydrolysate, bioconversion of the xylose, and recovery of xylitol from the fermented hydrolysate. There are relatively few reports on xylitol recovery from fermented media. In the present study, ion-exchange resins were used to clarify a fermented wheat straw hemicellulosic hydrolysate, which was then vacuum-concentrated and submitted to cooling in the presence of ethanol for xylitol crystallization. RESULTS: Sequential adsorption into two anion-exchange resins (A-860S and A-500PS) promoted considerable reductions in the content of soluble by-products (up to 97.5%) and in medium coloration (99.5%). Vacuum concentration led to a dark-colored viscous solution that inhibited xylitol crystallization. This inhibition could be overcome by mixing the concentrated medium with a commercial xylitol solution. Such a strategy led to xylitol crystals with up to 95.9% purity. The crystallization yield (43.5%) was close to that observed when using commercial xylitol solution (51.4%). CONCLUSION: The experimental data demonstrate the feasibility of using ion-exchange resins followed by cooling in the presence of ethanol as a strategy to promote the fast recovery and purification of xylitol from hemicellulose-derived fermentation media. (c) 2008 Society of Chemical Industry.

Flow boiling heat transfer of R134a and R245fa in a 2.3 mm tube

This paper presents new experimental flow boiling heat transfer results in micro-scale tubes. The experimental data were obtained in a horizontal 2.3 mm I.D stainless steel tube with heating length of 464 mm, R134a and R245fa as working fluids, mass velocities ranging from 50 to 700 kg m(-2) s(-1), heat flux from 5 to 55 kW m(-2), exit saturation temperatures of 22, 31 and 41 degrees C, and vapor qualities ranging from 0.05 to 0.99. Flow pattern characterization was also performed from images obtained by high-speed filming. Heat transfer coefficient results from 1 to 14 kW m(-2) K(-1) were measured. It was found that the heat transfer coefficient is a strong function of heat flux, mass velocity and vapor quality. The experimental data were compared against ten flow boiling predictive methods from the literature. Liu and Winterton [3], Zhang et al. [5] and Saitoh et al. [6] worked best for both fluids, capturing most of the experimental heat transfer trends. (C) 2010 Elsevier Ltd. All rights reserved.

On the accuracy of two-fluid model predictions for a particular gas-solid riser flow

Literature presents a huge number of different simulations of gas-solid flows in risers applying two-fluid modeling. In spite of that, the related quantitative accuracy issue remains mostly untouched. This state of affairs seems to be mainly a consequence of modeling shortcomings, notably regarding the lack of realistic closures. In this article predictions from a two-fluid model are compared to other published two-fluid model predictions applying the same Closures, and to experimental data. A particular matter of concern is whether the predictions are generated or not inside the statistical steady state regime that characterizes the riser flows. The present simulation was performed inside the statistical steady state regime. Time-averaged results are presented for different time-averaging intervals of 5, 10, 15 and 20 s inside the statistical steady state regime. The independence of the averaged results regarding the time-averaging interval is addressed and the results averaged over the intervals of 10 and 20 s are compared to both experiment and other two-fluid predictions. It is concluded that the two-fluid model used is still very crude, and cannot provide quantitative accurate results, at least for the particular case that was considered. (C) 2009 Elsevier Inc. All rights reserved.

On the compressive strength prediction for concrete masonry prisms

The results of a combined experimental program and numerical modeling program to evaluate the behavior of ungrouted hollow concrete blocks prisms under uniaxial compression are addressed. In the numerical program, three distinct approaches have been considered using a continuum model with a smeared approach, namely plane-stress, plane-strain and three-dimensional conditions. The response of the numerical simulations is compared with experimental data of masonry prisms using concrete blocks specifically designed for this purpose. The elastic and inelastic parameters were acquired from laboratory tests on concrete and mortar samples that constitute the blocks and the bed joint of the prisms. The results from the numerical simulations are discussed with respect to the ability to reproduce the global response of the experimental tests, and with respect to the failure behavior obtained. Good agreement between experimental and numerical results was found for the peak load and for the failure mode using the three-dimensional model, on four different sets of block/mortar types. Less good agreement was found for plain stress and plain strain models.

STRESS-STRAIN CURVES FOR STEEL FIBER-REINFORCED CONCRETE IN COMPRESSION

This paper presents a study on the compressive behavior of steel fiber-reinforced concrete. In this study, an analytical model for stress-strain curve for steel fiber-reinforced concrete is derived for concretes with strengths of 40 MPa and 60 MPa at the age of 28 days. Those concretes were reinforced with steel fibers with hooked ends 35 mm long and with aspect ratio of 65. The analytical model was compared with some experimental stress-strain curves and with some models reported in technical literature. Also, the accuracy of the proposed stress-strain curve was evaluated by comparison of the area under stress-strain curve. The results showed good agreement between analytical and experimental data and the benefits of the using of fibers in the compressive behavior of concrete.

Advanced process of microbiological control of wastewater in combined system of disinfection with UV radiation

The purpose of this study was to present a methodology with superior efficiency for inactivating pathogenic indicators commonly found in domestic sewage. The adopted method was based on synergistic effect resulting from the introduction of a UV radiation pre-disinfection stage of sewage followed by secondary treatment. A pilot unit was installed in the sewage treatment plant of the University of Sao Paulo to simulate the combined system in full-scale operational conditions. Its performance was evaluated through microbiological examinations for determining Escherichia coli, total coliforms and coliphages. The application of UV radiation at 5.1mW/cm(2) for 10 s of exposure in the first disinfection stage was enough to reduce the surviving number of E. coli around 100 times, in comparison to the conventional method. Therefore, based on experimental data, it is possible to conclude that combining treatment and pre-disinfection stage is an effective potential technique to produce effluents with lower degree of contamination by pathogenic organisms.

Stepped and smooth spillways: resistance effects on stilling basin lengths

The Darcy-Weisbach equation was used in the analysis of flow over spillways, furnishing theoretical tools to design stilling basins. Predictions for the length of hydraulic jump stilling basins downstream of stepped and smooth spillways are presented, together with ranges of values for the Darcy-Weisbach friction factor of both spillways. The experimental data were compared with results of the theoretical solution of the gradually varied flow equation. All comparisons were made in non-dimensional form. The values of the Darcy-Weisbach friction factor were roughly five times smaller for smooth spillways than for stepped spillways. The theoretical predictions and the experimental data allow to present approximate equations for a preliminary evaluation of the length and the bed level of hydraulic jump stilling basins. In the same way, approximate equations were presented for the evaluation of the friction factor in smooth and stepped spillways, as a function of the Froude number at the downstream cross-section.

Heterogeneous modeling of an anaerobic sequencing batch biofilm reactor (ASBBR)

The objective of this study was to estimate the first-order intrinsic kinetic constant (k(1)) and the liquid-phase mass transfer coefficient (k(c)) in a bench-scale anaerobic sequencing batch biofilm reactor (ASBBR) fed with glucose. A dynamic heterogeneous mathematical model, considering two phases (liquid and solid), was developed through mass balances in the liquid and solid phases. The model was adjusted to experimental data obtained from the ASBBR applied for the treatment of glucose-based synthetic wastewater with approximately 500 mg L-1 of glucose, operating in 8 h batch cycles, at 30 degrees C and 300 rpm. The values of the parameters obtained were 0.8911 min(-1) for k(1) and 0.7644 cm min(-1) for kc. The model was validated utilizing the estimated parameters with data obtained from the ASBBR operating in 3 h batch cycles, with a good representation of the experimental behavior. The solid-phase mass transfer flux was found to be the limiting step of the overall glucose conversion rate.

Solution of a heterogeneous modeling of a horizontal-flow anaerobic immobilized biomass (HAIB) reactor by the sequencing method

A modeling study was completed to develop a methodology that combines the sequencing and finite difference methods for the simulation of a heterogeneous model of a tubular reactor applied in the treatment of wastewater. The system included a liquid phase (convection diffusion transport) and a solid phase (diffusion reaction) that was obtained by completing a mass balance in the reactor and in the particle, respectively. The model was solved using a pilot-scale horizontal-flow anaerobic immobilized biomass (HAIB) reactor to treat domestic sewage, with the concentration results compared with the experimental data. A comparison of the behavior of the liquid phase concentration profile and the experimental results indicated that both the numerical methods offer a good description of the behavior of the concentration along the reactor. The advantage of the sequencing method over the finite difference method is that it is easier to apply and requires less computational time to model the dynamic simulation of outlet response of HAIB.