Numerical solution of the FENE-CR model in complex flows

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

A Numerical Study of the FENE-CR Model Applied to a Jet Flow Problem

The FENE-CR model is investigated through a numerical algorithm to simulate the time-dependent moving free surface flow produced by a jet impinging on a flat surface. The objective is to demonstrate that by increasing the extensibility parameter L, the numerical solutions converge to the solutions obtained with the Oldroyd-B model. The governing equations are solved by an established free surface flow solver based on the finite difference and marker-and-cell methods. Numerical predictions of the extensional viscosity obtained with several values of the parameter L are presented. The results show that if the extensibility parameter L is sufficiently large then the extensional viscosities obtained with the FENE-CR model approximate the corresponding Oldroyd-B viscosity. Moreover, the flow from a jet impinging on a flat surface is simulated with various values of the extensibility parameter L and the fluid flow visualizations display convergence to the Oldroyd-B jet flow results.

Development of a low-Reynolds-number k-ω model for FENE-P fluids

A low-Reynolds-number k-ω model for Newtonian fluids has been developed to predict drag reduction of viscoelastic fluids described by the FENE-P model. The model is an extension to viscoelastic fluids of the model for Newtonian fluids developed by Bredberg et al. (Int J Heat Fluid Flow 23:731-743, 2002). The performance of the model was assessed using results from direct numerical simulations for fully developed turbulent channel flow of FENE-P fluids. It should only be used for drag reductions of up to 50 % (low and intermediate drag reductions), because of the limiting assumption of turbulence isotropy leading to an under-prediction of k, but compares favourably with results from k-ε models in the literature based on turbulence isotropy. © 2012 Springer Science+Business Media Dordrecht.

Optimizing the size of the area surveyed for monitoring a Eurasian lynx (Lynx lynx) population in the Swiss Alps by means of photographic capture-recapture

We studied the influence of surveyed area size on density estimates by means of camera-trapping in a low-density felid population (1-2 individuals/100 km(2) ). We applied non-spatial capture-recapture (CR) and spatial CR (SCR) models for Eurasian lynx during winter 2005/2006 in the northwestern Swiss Alps by sampling an area divided into 5 nested plots ranging from 65 to 760 km(2) . CR model density estimates (95% CI) for models M0 and Mh decreased from 2.61 (1.55-3.68) and 3.6 (1.62-5.57) independent lynx/100 km(2) , respectively, in the smallest to 1.20 (1.04-1.35) and 1.26 (0.89-1.63) independent lynx/100 km(2) , respectively, in the largest area surveyed. SCR model density estimates also decreased with increasing sampling area but not significantly. High individual range overlaps in relatively small areas (the edge effect) is the most plausible reason for this positive bias in the CR models. Our results confirm that SCR models are much more robust to changes in trap array size than CR models, thus avoiding overestimation of density in smaller areas. However, when a study is concerned with monitoring population changes, large spatial efforts (area surveyed ≥760 km(2) ) are required to obtain reliable and precise density estimates with these population densities and recapture rates.

Effects of the Er,Cr:YSGG laser on bone and soft tissue in a rat model

The purpose of this study was to investigate the histological changes that occur in rat soft and hard tissues after Er,Cr:YSGG laser surgery. Each of 20 rats was submitted to four procedures which were randomly distributed to the right and left sides of the animal: procedure 1 dorsal incision with a scalpel; procedure 2 dorsal incision with a 2.0-W Er,Cr:YSGG laser; procedure 3 skull defect created with a diamond bur; procedure 4 skull defect created with a 3.0-W Er,Cr:YSGG laser. The animals were killed 3, 7, 15 and 30 days after surgery, and histological examinations were performed. The histometric analysis of the bone defects was evaluated using an unpaired t-test. Initially, the dorsum showed more histological signs of repair following procedure 1, although similar healing responses following procedures 1 and 2 were seen on day 30 after surgery. By day 30 the bone formation observed following procedure 4 was much more evident than following procedure 3. The unpaired t-test identified significant differences in bone formation on day 30 (p = 0.01), whereas a greater bone percentage was seen following procedure 4 than following procedure 3 (79.96 +/- 10.30% and 58.23 +/- 9.99%, respectively). Thus, histological repair of the Er,Cr:YSGG laser wounds was similar to that of the scalpel wounds. However, skull defects created with the Er,Cr:YSGG laser showed greater bone formation than defects created with the bur. Within the limitations of this study, we can conclude that the Er,Cr:YSGG laser is a promising surgical instrument in vivo, particularly for bone surgery.

Three-dimensional finite element thermal analysis of dental tissues irradiated with Er,Cr:YSGG laser

In the present study, a finite element model of a half-sectioned molar tooth was developed in order to understand the thermal behavior of dental hard tissues (both enamel and dentin) under laser irradiation. The model was validated by comparing it with an in vitro experiment where a sound molar tooth was irradiated by an Er,Cr:YSGG pulsed laser. The numerical tooth model was conceived to simulate the in vitro experiment, reproducing the dimensions and physical conditions of the typical molar sound tooth, considering laser energy absorption and calculating the heat transfer through the dental tissues in three dimensions. The numerical assay considered the same three laser energy densities at the same wavelength (2.79 mu m) used in the experiment. A thermographic camera was used to perform the in vitro experiment, in which an Er, Cr: YSGG laser (2.79 mu m) was used to irradiate tooth samples and the infrared images obtained were stored and analyzed. The temperature increments in both the finite element model and the in vitro experiment were compared. The distribution of temperature inside the tooth versus time plotted for two critical points showed a relatively good agreement between the results of the experiment and model. The three dimensional model allows one to understand how the heat propagates through the dentin and enamel and to relate the amount of energy applied, width of the laser pulses, and temperature inside the tooth. (C) 2008 American Institute of Physics. [DOI: 10.1063/1.2953526]

Adsorption of Cr(VI) from aqueous solution by hydrous zirconium oxide

A type of ZrO(2)center dot nH(2)O Was synthesized and its Cr(VI) removal potential was investigated in this study. The kinetic study, adsorption isotherm, pH effect, thermodynamic study and desorption were examined in batch experiments. The kinetic process was described by a pseudo-second-order rate model very well. The Cr(VI) adsorption tended to increase with a decrease of pH. The adsorption data fitted well to the Langmuir model. The adsorption capacity increased from 61 to 66 mg g(-1) when the temperature was increased from 298 to 338 K. The positive values of both Delta H degrees and Delta S degrees suggest an endothermic reaction and increase in randomness at the solid-liquid interface during the adsorption. Delta G degrees values obtained were negative indicating a spontaneous adsorption process. The effective desorption of Cr(VI) on ZrO(2)center dot nH(2)O could be achieved using distilled water at pH 12. (C) 2009 Elsevier B.V. All rights reserved.

Thermodynamic self-consistency issues related to the Cluster Variation Method: The case of the BCC Cr-Fe (Chromium-Iron) system

The Cluster Variation Method (CVM), introduced over 50 years ago by Prof. Dr. Ryoichi Kikuchi, is applied to the thermodynamic modeling of the BCC Cr-Fe system in the irregular tetrahedron approximation, using experimental thermochemical data as initial input for accessing the model parameters. The results are checked against independent data on the low-temperature miscibility gap, using increasingly accurate thermodynamic models, first by the inclusion of the magnetic degrees of freedom of iron and then also by the inclusion of the magnetic degrees of freedom of chromium. It is shown that a reasonably accurate description of the phase diagram at the iron-rich side (i.e. the miscibility gap borders and the Curie line) is obtained, but only at expense of the agreement with the above mentioned thermochemical data. Reasons for these inconsistencies are discussed, especially with regard to the need of introducing vibrational degrees of freedom in the CVM model. (C) 2008 Elsevier Ltd. All rights reserved.

Isolated limb perfusion with melphalan for human melanoma xenografts in the hindlimb of nude rats: A surviving animal model

We have established a surviving model of isolated limb perfusion using xenografts of the human melanoma cell line MM 96L injected subcutaneously into the hindlimb of a nude rat, The femoral artery and vein were cannulated via the left renal artery and vein and the hind limb was isolated using tourniquets. The limb was perfused with Krebs Heinseleit buffer at 37 degrees C containing 4.7% bovine serum albumin at a constant flow rate of 4 mi per min for 30-60 min with 100% survival of the animals, Tumour vascularization and blood flow were demonstrated using vascular casts and [Cr-51]-microspheres. Following the addition of melphalan (15 or 100 mu g/ml), drug concentrations in the perfusate, tissues and systemic circulation were determined using high pressure liquid chromatography (HPLC), Systemic leakage, assessed using [I-125]albumin and melphalan and detected by a gamma-counter and HPLC respectively, was <0.5%. The melphalan concentration and tissue flow rate in the tumour deposits were 40 and 30% respectively, when compared with the surrounding subcutaneous tissue, At a dose of 15 mu g/ml, melphalan caused a reduction in tumour growth after 60 min perfusion, and a significant reduction in tumour size was seen when the melphalan dose was 100 mu g/ml. The surviving nude rat model of isolated limb perfusion for recurrent melanoma will allow examination of optimal perfusion conditions, along with the pharmacokinetics, pharmacodynamics and efficacy of melphalan and other drugs.

Protective effect of octreotide and infliximab in an experimental model of indomethacin-induced inflammatory bowel disease

Indomethacin administration in animals increases permeability of the small intestine, leading to inflammation that mimics Crohn`s disease. Nonsteroidal anti-inflammatory drugs increase the permeability of the intestinal epithelial barrier and should therefore be used with caution in patients with Crohn`s disease. We analyzed the protective effects of octreotide and the tumor necrosis factor-alpha inhibitor infliximab in a rat model of indomethacin-induced enterocolitis. Male Wistar rats received 20 mg of infliximab or 10 mu g of octreotide 24 h prior to injection with indomethacin. Intestinal permeability was analyzed using Cr-51-ethylenediaminetetraacetic acid clearance. No microscopic or macroscopic alterations were observed in the rats receiving infliximab or octreotide, both of which increased permeability (P < 0.001 versus controls). Our macroscopic and microscopic findings might be related to the low specificity of infliximab and suggest that cytokines affect the intestinal epithelial barrier, as evidenced by the protective effect that infliximab had on the permeability parameters evaluated.

Using a NPWE model observer to assess suitable image quality for a digital mammography quality assurance programme.

A method of objectively determining imaging performance for a mammography quality assurance programme for digital systems was developed. The method is based on the assessment of the visibility of a spherical microcalcification of 0.2 mm using a quasi-ideal observer model. It requires the assessment of the spatial resolution (modulation transfer function) and the noise power spectra of the systems. The contrast is measured using a 0.2-mm thick Al sheet and Polymethylmethacrylate (PMMA) blocks. The minimal image quality was defined as that giving a target contrast-to-noise ratio (CNR) of 5.4. Several evaluations of this objective method for evaluating image quality in mammography quality assurance programmes have been considered on computed radiography (CR) and digital radiography (DR) mammography systems. The measurement gives a threshold CNR necessary to reach the minimum standard image quality required with regards to the visibility of a 0.2-mm microcalcification. This method may replace the CDMAM image evaluation and simplify the threshold contrast visibility test used in mammography quality.

A MODEL OF CREATINE DEFICIENCY SYNDROMES IN 3D BRAIN CELL CULTURES BY KNOCKDOWN OF GAMT AND SLC6A8 GENES

La créatine joue un rôle essentiel dans le métabolisme cellulaire par sa conversion, par la creatine kinase, en phosphocreatine permettant la régénération de l'ATP. La synthèse de créatine, chez les mammifères, s'effectue par une réaction en deux étapes impliquant Γ arginine: glycine amidinotransférase (AGAT) et la guanidinoacétate méthyltransférase (GAMT). L'entrée de créatine dans les cellules s'effectue par son transporteur, SLC6A8. Les déficiences en créatine, dues au déficit en GAMT, AGAT ou SLC6A8, sont fréquentes et caractérisées par une absence ou une forte baisse de créatine dans le système nerveux central. Alors qu'il est connu que AGAT, GAMT et SLC6A8 sont exprimés par le cerveau, les conséquences des déficiences en créatine sur les cellules nerveuses sont peu comprises. Le but de ce travail était de développer de nouveaux modèles expérimentaux des déficiences en Cr dans des cultures 3D de cellules nerveuses de rat en agrégats au moyen de l'interférence à l'ARN appliquée aux gènes GAMT et SLC6A8. Des séquences interférentes (shRNAs) pour les gènes GAMT et SLC6A8 ont été transduites par des vecteurs viraux AAV (virus adéno-associés), dans les cellules nerveuses en agrégats. Nous avons ainsi démontré une baisse de l'expression de GAMT au niveau protéique (mesuré par western blot), et ARN messager (mesuré par qPCR) ainsi qu'une variation caractérisitique de créatine et guanidinoacétate (mesuré par spectrométrie de masse). Après avoir validé nos modèles, nous avons montré que les knockdown de GAMT ou SLC6A8 affectent le développement des astrocytes et des neurones ou des oligodendrocytes et des astrocytes, respectivement, ainsi qu'une augmentation de la mort cellulaire et des modifications dans le pattern d'activation des voies de signalisation impliquant caspase 3 et p38 MAPK, ayant un rôle dans le processus d'apoptose. - Creatine plays essential roles in energy metabolism by the interconversion, by creatine kinase, to its phosphorylated analogue, phosphocreatine, allowing the regeneration of ATP. Creatine is synthesized in mammals by a two step mechanism involving arginine:glycine amidinotransferase (AGAT) and guanidinoacetate methyltransferase (GAMT). Creatine is taken up by cells by a specific transporter, SLC6A8. Creatine deficiency syndromes, due to defects in GAMT, AGAT and SLC6A8, are among the most frequent inborn errors of metabolism, and are characterized by an absence or a severe decrease of creatine in central nervous system, which is the main tissue affected. While it is known that AGAT, GAMT and SLC6A8 are expressed in CNS, many questions remain on the specific effects of AGAT, GAMT and SLC6A8 deficiencies on brain cells. Our aim was to develop new experimental models of creatine deficiencies by knockdown of GAMT and SLC6A8 genes by RNAi in 3D organotypic rat brain cell cultures in aggregates. Specific shRNAs for the GAMT and SLC6A8 genes were transduced in brain cell aggregates by adeno-associated viruses (AAV). The AAV-transduced shRNAs were able to efficiently knockdown the expression of our genes of interest, as shown by a strong decrease of protein by western blotting, a decrease of mRNA by qPCR or characteristic variations of creatine and guanidinoacetate by tandem mass spectrometry. After having validated our experimental models, we have also shown that GAMT and SLC6A8 knockdown affected the development of astrocytes and neurons or oligodendrocytes and astrocytes, respectively. We also observed an increase of cell death and variations in activation pattern of caspase 3 and p38 MAPK pathways, involved in apoptosis, in our experimental model.

Creatine deficiency syndomes : a new model of partial GAMT deficiency affecting brain cell development

Les syndromes de déficiences cérébrales en créatine (CCDS) sont dus à des mutations dans les gènes GATM et G AMT (codant pour les enzymes AGAT et G AMT de la voie de synthèse de créatine) ainsi que SLC6A8 (transporteur de créatine), et génèrent une absence ou une très forte baisse de créatine (Cr) dans le cerveau, mesurée par spectroscopic de résonance magnétique. Les patients CCDS développent des handicaps neurologiques sévères. Les patients AGAT et GAMT peuvent être traités avec des doses importantes de Cr, mais gardent dans la plupart des cas des séquelles neurologiques irréversibles. Aucun traitement efficace n'existe à ce jour pour la déficience en SLC6A8. Bien que de nombreux modèles aient été développés pour comprendre la Cr cérébrale en conditions physiologiques, les pathomécanismes des CCDS ne sont pas encore compris. Des souris transgéniques pour les gènes Gatm, Gamt et Slc6a8 ont été générées, mais elles ne miment que partiellement la pathologie humaine. Parmi les CCDS, la déficience en GAMT est la plus sévère, en raison de l'accumulation cérébrale de l'intermédiaire guanidinoacétate (GAA). Alors que la toxicité cérébrale du GAA a été étudiée par exposition directe au GAA d'animaux adultes sains, les mécanismes de la toxicité du GAA en condition de déficience en GAMT dans le cerveau en développement sont encore inconnus. Le but de ce projet était donc de développer un modèle de déficience en GAMT dans des cultures 3D primaires de cellules nerveuses de rat en agrégats par knock-down du gène GAMT, en utilisant un virus adéno-associé (AAV) induisant le mécanisme d'interférence à l'ARN (RNAi). Le virus scAAV2, à la multiplicité d'infection de 1000, s'est révélé le plus efficace pour transduire tous les types de cellules nerveuses des cultures (neurones, astrocytes, oligodendrocytes), et générer un knock-down maximal de la protéine GAMT de 85% (jour in vitro 18). Cette déficience partielle en GAMT s'est révélée insuffisante pour générer une déficience en Cr, mais a causé l'accumulation attendue de GAA, à des doses comparables aux niveaux observés dans le LCR des patients GAMT. Le GAA a induit une croissance axonale anarchique accompagnée d'une baisse de l'apoptose naturelle, suivis par une induction tardive de mort cellulaire non-apoptotique. Le co-traitement par la Cr a prévenu tous les effets toxiques du GAA. Ce travail montre que l'accumulation de GAA en absence de déficience en Cr est suffisante pour affecter le développement du tissu nerveux, et suggère que des formes de déficiences en GAMT supplémentaires, ne présentant pas de déficiences en Cr, pourraient être découvertes par mesure du GAA, en particulier à travers les programmes récemment proposés de dépistage néonatal de la déficience en GAMT. -- Cerebral creatine deficiency syndromes (CCDS) are caused by mutations in the genes GATM and GAMT (respectively coding for the two enzymes of the creatine synthetic pathway, AGAT and GAMT) as well as SLC6A8 (creatine transporter), and lead to the absence or very strong decrease of creatine (Cr) in the brain when measured by magnetic resonance spectroscopy. Affected patients show severe neurological impairments. While AGAT and GAMT deficient patients can be treated with high dosages of Cr, most remain with irreversible brain sequelae. No treatment has been successful so far for SLC6A8 deficiency. While many models have helped understanding the cerebral Cr pathways in physiological conditions, the pathomechanisms underlying CCDS are yet to be elucidated. Transgenic mice carrying mutations in the Gatm, Gamt and Slc6a8 genes have been developed, but only partially mimic the human pathology. Among CCDS, GAMT deficiency is the most severe, due to the CNS accumulation of the guanidinoacetate (GAA) intermediate. While brain toxicity of GAA has been explored through direct GAA exposure of adult healthy animals, the mechanisms underlying GAA toxicity in GAMT deficiency conditions on the developing CNS are yet unknown. The aim of this project was thus to develop and characterize a GAMT deficiency model in developing brain cells by gene knockdown, by adeno-associated virus (AAV)-driven RNA interference (RNAi) in rat 3D organotypic primary brain cell cultures in aggregates. scAAV2 with a multiplicity of infection of 1000 was shown as the most efficient serotype, was able to transduce all brain cell types (neurons, astrocytes, oligodendrocytes) and to induce a maximal GAMT protein knockdown of 85% (day in vitro 18). Metabolite analysis showed that partial GAMT knockdown was insufficient to induce Cr deficiency but generated the awaited GAA accumulation at concentrations comparable to the levels observed in cerebrospinal fluid of GAMT-deficient patients. Accumulated GAA induced axonal hypersprouting paralleled with inhibition of natural apoptosis, followed by a later induction in non-apoptotic cell death. Cr supplementation led to the prevention of all GAA-induced toxic effects. This work shows that GAA accumulation without Cr deficiency is sufficient to affect CNS development, and suggests that additional partial GAMT deficiencies, which may not show the classical brain Cr deficiency, may be discovered through GAA measurement including by recently proposed neonatal screening programs for GAMT deficiency.

Adsorção de Cr(VI) em esferas reticuladas de quitosana: novas correlações cinéticas e termodinâmicas utilizando microcalorimetria isotérmica contínua

The synthesis and characterization of crosslinked chitosan microbeads and their application in the removal of Cr(VI) are described. New kinetic and thermodynamic parameters of Cr(VI) adsorptions processes were found using continuous isothermal calorimetry. All adsorption processes are exothermic in nature. However, a multivariate statistical analysis have pointed out that adsorption enthalpies were affected by important binary interactions of the initial Cr(VI) in solution and temperature. The adsorption energetic data were well fitted to a kinetic exponential model, which have indicated fractionary adsorption kinetic orders.

Preparation and evaluation of magnetic chitosan particles modified with ethylenediamine and Fe(III) for the removal of Cr(VI) from aqueous solutions

The adsorption of Cr(VI) in aqueous solution by magnetic particles of crosslinked chitosan-ethylenediamine-Fe(III) (MPCh-EDA-FeCL) was studied in a batch system. Fe3+ in the MPCh-EDA-FeCL permitted that adsorption of Cr(VI) occurred with maximum efficiency between pH 3 and 11. The maximum adsorption capacity at pH 7.0 was 81.04 mg g-1 at 25 ºC. The adsorption kinetic process was described by the pseudo-second-order model. Thermodynamic parameters indicated spontaneous, exothermic and chemical adsorption nature. The adsorbent was successively regenerated using a 0.1 mol L-1 NaOH solution. Results were satisfactory for treatment of wastewater from the electroplating industry.