Melanin as an active layer in biosensors

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

The smear layer created by scaling and root planing is physiologically eliminated in a biphasic process

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Cross-Layer Packet Size Optimization for Wireless Terrestrial, Underwater, and Underground Sensor Networks

In this paper, a cross-layer solution for packet size optimization in wireless sensor networks (WSN) is introduced such that the effects of multi-hop routing, the broadcast nature of the physical wireless channel, and the effects of error control techniques are captured. A key result of this paper is that contrary to the conventional wireless networks, in wireless sensor networks, longer packets reduce the collision probability. Consequently, an optimization solution is formalized by using three different objective functions, i.e., packet throughput, energy consumption, and resource utilization. Furthermore, the effects of end-to-end latency and reliability constraints are investigated that may be required by a particular application. As a result, a generic, cross-layer optimization framework is developed to determine the optimal packet size in WSN. This framework is further extended to determine the optimal packet size in underwater and underground sensor networks. From this framework, the optimal packet sizes under various network parameters are determined.

Biological, physical and chemical properties at the Subtropical Shelf Front Zone in the SW Atlantic Continental Shelf

The physical aspects of the Subtropical Shelf Front (STSF) for the Southwest Atlantic Continental Shelf were previously described. However, only scarce data on the biology of the front is available in the literature. The main goal of this paper is to describe the physical, chemical and biological properties of the STSF found in winter 2003 and summer 2004. A cross-section was established at the historically determined location of the STSF. Nine stations were sampled in winter and seven in summer. Each section included a series of conductivity-temperature-depth (CTD) stations where water samples from selected depths were filtered for nutrient determination. Surface samples were taken for chlorophyll a (Chl-a) determination and plankton net tows carried out above and below the pycnocline. Results revealed that winter was marked by an inner-shelf salinity front and that the STSF was located on the mid-shelf The low salinity waters in the inner-shelf indicated a strong influence of freshwater, with high silicate (72 mu M), suspended matter (45 mg l(-1)), phosphate (2.70 mu M) and low nitrate (1.0 mu M) levels. Total dissolved nitrogen was relatively high (22.98 mu M), probably due to the elevated levels of organic compound contribution close to the continental margin. Surface Chl-a concentration decreased from coastal well-mixed waters, where values up to 8.0 mg m(-3) were registered, to offshore waters. Towards the open ocean, high subsurface nutrients values were observed, probably associated to South Atlantic Central Waters (SACW). Zooplankton and ichthyoplankton abundance followed the same trend; three different groups associated to the inner-, mid- and outer-shelf region were identified. During summer, diluted waters extended over the shelf to join the STSF in the upper layer; the concentration of inorganic nutrients decreased in shallow waters; however, high values were observed between 40 and 60 m and in deep offshore waters. Surface Chl-a ranged 0.07-1.5 mg m(-3); winter levels were higher. Three groups of zoo and ichthyoplankton, separated by the STSF, were also identified. Results of the study performed suggest that the influence of freshwater was stronger during winter and that abundance distribution of Chl-a, copepods and ichthyoplankton was related to the Plata Plume Waters (PPW), rather than to the presence of the STSF. During summer, when the presence of freshwater decreases, plankton interactions seem to take place in the STSF. (C) 2008 Elsevier Ltd. All rights reserved.

Different protocols of physical exercise produce different effects on synaptic and structural proteins in motor areas of the rat brain

The plastic brain responses generated by the training with acrobatic exercise (AE) and with treadmill exercise (TE) may be different. We evaluated the protein expression of synapsin I (SYS), synaptophysin (SYP), microtubule-associated protein 2 (MAP2) and neurofilaments (NF) by immunohistochemistry and Western blotting in the motor cortex, striatum and cerebellum of rats subjected to TE and AE. Young adult male Wistar rats were divided into 3 groups: sedentary (Sed) (n=15), TE (n=20) and AE (n=20). The rats were trained 3 days/week for 4 weeks on a treadmill at 0.6 km/h, 40 min/day (TE), or moved through a circuit of obstacles 5 times/day (AE). The rats from the TE group exhibited a significant increase of SYS and SYP in the motor cortex, of NF68, SYS and SYP in the striatum, and of MAP2, NF and SYS in the cerebellum, whereas NF was decreased in the motor cortex and the molecular layer of the cerebellar cortex. On the other hand, the rats from the AE group showed a significant increase of MAP2 and SYP in the motor cortex, of all four proteins in the striatum, and of SYS in the cerebellum. In conclusion, AE induced changes in the expression of synaptic and structural proteins mainly in the motor cortex and striatum, which may underlie part of the learning of complex motor tasks. TE, on the other hand, promoted more robust changes of structural proteins in all three regions, especially in the cerebellum, which is involved in learned and automatic tasks. (C) 2012 Elsevier B.V. All rights reserved.

Electrodeposition of catalytic and magnetic gold nanoparticles on dendrimer-carbon nanotube layer-by-layer films

Magnetic and catalytic gold nanoparticles were electrodeposited through potential pulse on dendrimer-carbon nanotube layer-by-layer (LbL) films. A plasmon absorption band at about 550 nm revealed the presence of nanoscale gold in the film. The location of the Au nanoparticles in the film was clearly observed by selecting the magnetic force microscopy mode. To our knowledge, this is the first report on the electrochemical synthesis of magnetic Au nanoparticles. In addition to the magnetic properties, the Au nanoparticles also exhibited high catalytic activity towards ethanol and glycerol oxidation in alkaline medium.

Spectroscopic, morphological and electrochromic characterization of layer-by-layer hybrid films of polyaniline and hexaniobate nanoscrolls

The combination of semiconducting oxides and polyaniline in the nanoscale range may result in hybrid materials having enhanced properties, such as electrochromism and charge capacity. This paper reports the spectroscopic, morphological and electrochromic characterization of hybrid films made up of hexaniobate one-dimensional (1D) nanoscrolls and polyaniline prepared by the layer-by-layer assembly technique (LbL). Secondary electron imaging and backscattered electron imaging techniques performed using a scanning electron microscope showed that polyaniline is adsorbed on the hexaniobate nanoscrolls, which confirms the combination of the components in the nanoscale domain. UV-VIS-NIR electronic spectra of the LbL hybrid films showed the absorption tail in the NIR region, assigned to delocalized polarons of the polyaniline. Resonance Raman spectra in the 1000-1700 cm(-1) range indicated that hybrid films present a higher relative intensity of polaron bands at 1337 and 1508 cm(-1) than pristine polyaniline in the emeraldine salt form. These results suggest that hexaniobate nanoscrolls induce a secondary doping of polyaniline. The cyclic voltammetry (CV) data for the hybrid film showed a specific capacity of 870 C cm(-3). According to CV results, the synergistic effect on charge storage properties of the hybrid material is attributed to the enhanced electroactivity of the hexaniobate component in the LbL film. Spectroelectrochemical experiments showed that the electrochromic efficiencies at 420 nm are ca. -41 and 24 cm(2) C-1 as the potential changes from 0.8 to -0.9 V and from -0.9 to -1.8 V, respectively, whereas at 800 nm the efficiencies are ca. -55 and 8 cm(2) C-1 for the same potential ranges. The electrochromic efficiencies and multi-colour character of the LbL film of hexaniobate nanoscrolls and polyaniline indicate that this novel hybrid material is an interesting modified electrode for electrochromic devices.

Modelling coupled physical-biogeochemical processes in ice-covered oceans

The last decades have seen a large effort of the scientific community to study and understand the physics of sea ice. We currently have a wide - even though still not exhaustive - knowledge of the sea ice dynamics and thermodynamics and of their temporal and spatial variability. Sea ice biogeochemistry is instead largely unknown. Sea ice algae production may account for up to 25% of overall primary production in ice-covered waters of the Southern Ocean. However, the influence of physical factors, such as the location of ice formation, the role of snow cover and light availability on sea ice primary production is poorly understood. There are only sparse localized observations and little knowledge of the functioning of sea ice biogeochemistry at larger scales. Modelling becomes then an auxiliary tool to help qualifying and quantifying the role of sea ice biogeochemistry in the ocean dynamics. In this thesis, a novel approach is used for the modelling and coupling of sea ice biogeochemistry - and in particular its primary production - to sea ice physics. Previous attempts were based on the coupling of rather complex sea ice physical models to empirical or relatively simple biological or biogeochemical models. The focus is moved here to a more biologically-oriented point of view. A simple, however comprehensive, physical model of the sea ice thermodynamics (ESIM) was developed and coupled to a novel sea ice implementation (BFM-SI) of the Biogeochemical Flux Model (BFM). The BFM is a comprehensive model, largely used and validated in the open ocean environment and in regional seas. The physical model has been developed having in mind the biogeochemical properties of sea ice and the physical inputs required to model sea ice biogeochemistry. The central concept of the coupling is the modelling of the Biologically-Active-Layer (BAL), which is the time-varying fraction of sea ice that is continuously connected to the ocean via brines pockets and channels and it acts as rich habitat for many microorganisms. The physical model provides the key physical properties of the BAL (e.g., brines volume, temperature and salinity), and the BFM-SI simulates the physiological and ecological response of the biological community to the physical enviroment. The new biogeochemical model is also coupled to the pelagic BFM through the exchange of organic and inorganic matter at the boundaries between the two systems . This is done by computing the entrapment of matter and gases when sea ice grows and release to the ocean when sea ice melts to ensure mass conservation. The model was tested in different ice-covered regions of the world ocean to test the generality of the parameterizations. The focus was particularly on the regions of landfast ice, where primary production is generally large. The implementation of the BFM in sea ice and the coupling structure in General Circulation Models will add a new component to the latters (and in general to Earth System Models), which will be able to provide adequate estimate of the role and importance of sea ice biogeochemistry in the global carbon cycle.

The Effect of Preservative Interventions on the Chemical- Physical and Structural Characteristics of Panel Painting

This work studies the impact of two traditional Romanian treatments, Red Petroleum and Propolis, in terms of real efficiency and consequence on the wooden artifacts. The application of these solutions is still a widely adopted and popular technique in preservative conservation but the impact of these solutions is not well known. It is important to know the effect of treatments on chemical-physical and structural characteristics of the artifacts, not only for understanding the influence on present conditions but also for foreseeing the future behavior. These treatments with Romanian traditional products are compared with a commercial antifungal product, Biotin R, which is utilized as reference to control the effectiveness of Red Petroleum and Propolis. Red Petroleum and Propolis are not active against mould while Biotin R is very active. Mould attack is mostly concentrated in the painted layer, where the tempera, containing glue and egg, enhance nutrition availability for moulds. Biotin R, even if is not a real insecticide but a fungicide, was the most active product against insect attack of the three products, followed by Red Petroleum, Propolis and untreated reference. As for colour, it did not change so much after the application of Red Petroleum and Biotin R and the colour difference was almost not perceptible. On the contrary, Propolis affected the colour a lot. During the exposure at different RH, the colour changes significantly at 100% RH at equilibrium and this is mainly due to the mould attack. Red Petroleum penetrates deeply into wood, while Propolis does not penetrate and remains only on the surface. However, Red Petroleum does not interact chemically with wood substance and it is easy volatilized in oven-dry condition. On the contrary Propolis interacts chemically with wood substance and hardly volatilized, even in oven-dry condition and consequently Propolis remains where it penetrated, mostly on the surface. Treatment by immersion has impact on wood physical parameters while treatment by brushing does not have significant impact. Especially Red Petroleum has an apparent impact on moisture content (MC) due to the penetration of solution, while Propolis does not penetrate so much and remains only on surface therefore Propolis does not have so much impact as Red Petroleum. However, if the weight of the solution penetrated in wood is eliminated, there is not significant difference in MC between treated and untreated samples. Considering physical parameters, dimensional stability is an important parameter. The variation of wood moisture content causes shrinkages/swelling of the wood that polychrome layer can only partially follow. The dimension of wooden supports varied under different moisture conditioning; the painted layer cannot completely follow this deformation, and consequently a degradation and deterioration caused by detachment, occurs. That detachment affects the polychrome stratification of the panel painting and eventually the connections between the different layer compositions of the panel painting.

Detection and Modeling of Boundary Layer Height

This thesis tackles the problem of the automated detection of the atmospheric boundary layer (BL) height, h, from aerosol lidar/ceilometer observations. A new method, the Bayesian Selective Method (BSM), is presented. It implements a Bayesian statistical inference procedure which combines in an statistically optimal way different sources of information. Firstly atmospheric stratification boundaries are located from discontinuities in the ceilometer back-scattered signal. The BSM then identifies the discontinuity edge that has the highest probability to effectively mark the BL height. Information from the contemporaneus physical boundary layer model simulations and a climatological dataset of BL height evolution are combined in the assimilation framework to assist this choice. The BSM algorithm has been tested for four months of continuous ceilometer measurements collected during the BASE:ALFA project and is shown to realistically diagnose the BL depth evolution in many different weather conditions. Then the BASE:ALFA dataset is used to investigate the boundary layer structure in stable conditions. Functions from the Obukhov similarity theory are used as regression curves to fit observed velocity and temperature profiles in the lower half of the stable boundary layer. Surface fluxes of heat and momentum are best-fitting parameters in this exercise and are compared with what measured by a sonic anemometer. The comparison shows remarkable discrepancies, more evident in cases for which the bulk Richardson number turns out to be quite large. This analysis supports earlier results, that surface turbulent fluxes are not the appropriate scaling parameters for profiles of mean quantities in very stable conditions. One of the practical consequences is that boundary layer height diagnostic formulations which mainly rely on surface fluxes are in disagreement to what obtained by inspecting co-located radiosounding profiles.

The atmospheric stable boundary layer: Data analysis and comparison with similarity theories

The objective of this dissertation is to study the structure and behavior of the Atmospheric Boundary Layer (ABL) in stable conditions. This type of boundary layer is not completely well understood yet, although it is very important for many practical uses, from forecast modeling to atmospheric dispersion of pollutants. We analyzed data from the SABLES98 experiment (Stable Atmospheric Boundary Layer Experiment in Spain, 1998), and compared the behaviour of this data using Monin-Obukhov's similarity functions for wind speed and potential temperature. Analyzing the vertical profiles of various variables, in particular the thermal and momentum fluxes, we identified two main contrasting structures describing two different states of the SBL, a traditional and an upside-down boundary layer. We were able to determine the main features of these two states of the boundary layer in terms of vertical profiles of potential temperature and wind speed, turbulent kinetic energy and fluxes, studying the time series and vertical structure of the atmosphere for two separate nights in the dataset, taken as case studies. We also developed an original classification of the SBL, in order to separate the influence of mesoscale phenomena from turbulent behavior, using as parameters the wind speed and the gradient Richardson number. We then compared these two formulations, using the SABLES98 dataset, verifying their validity for different variables (wind speed and potential temperature, and their difference, at different heights) and with different stability parameters (zita or Rg). Despite these two classifications having completely different physical origins, we were able to find some common behavior, in particular under weak stability conditions.

Properties of basal dendrites of layer 5 pyramidal neurons: a direct patch-clamp recording study

Basal dendrites receive the majority of synapses that contact neocortical pyramidal neurons, yet our knowledge of synaptic processing in these dendrites has been hampered by their inaccessibility for electrical recordings. A new approach to patch-clamp recordings enabled us to characterize the integrative properties of these cells. Despite the short physical length of rat basal dendrites, synaptic inputs were electrotonically remote from the soma (>30-fold excitatory postsynaptic potential (EPSP) attenuation) and back-propagating action potentials were significantly attenuated. Unitary EPSPs were location dependent, reaching large amplitudes distally (>8 mV), yet their somatic contribution was relatively location independent. Basal dendrites support sodium and NMDA spikes, but not calcium spikes, for 75% of their length. This suggests that basal dendrites, despite their proximity to the site of action potential initiation, do not form a single basal-somatic region but rather should be considered as a separate integrative compartment favoring two integration modes: subthreshold, location-independent summation versus local amplification of incoming spatiotemporally clustered information.

Filtration and oxidation characteristics of a diesel oxidation catalyst and a catalyzed particulate filter : development of a 1-D 2-layer model

The emissions, filtration and oxidation characteristics of a diesel oxidation catalyst (DOC) and a catalyzed particulate filter (CPF) in a Johnson Matthey catalyzed continuously regenerating trap (CCRT ®) were studied by using computational models. Experimental data needed to calibrate the models were obtained by characterization experiments with raw exhaust sampling from a Cummins ISM 2002 engine with variable geometry turbocharging (VGT) and programmed exhaust gas recirculation (EGR). The experiments were performed at 20, 40, 60 and 75% of full load (1120 Nm) at rated speed (2100 rpm), with and without the DOC upstream of the CPF. This was done to study the effect of temperature and CPF-inlet NO2 concentrations on particulate matter oxidation in the CCRT ®. A previously developed computational model was used to determine the kinetic parameters describing the oxidation characteristics of HCs, CO and NO in the DOC and the pressure drop across it. The model was calibrated at five temperatures in the range of 280 – 465° C, and exhaust volumetric flow rates of 0.447 – 0.843 act-m3/sec. The downstream HCs, CO and NO concentrations were predicted by the DOC model to within ±3 ppm. The HCs and CO oxidation kinetics in the temperature range of 280 - 465°C and an exhaust volumetric flow rate of 0.447 - 0.843 act-m3/sec can be represented by one ’apparent’ activation energy and pre-exponential factor. The NO oxidation kinetics in the same temperature and exhaust flow rate range can be represented by ’apparent’ activation energies and pre-exponential factors in two regimes. The DOC pressure drop was always predicted within 0.5 kPa by the model. The MTU 1-D 2-layer CPF model was enhanced in several ways to better model the performance of the CCRT ®. A model to simulate the oxidation of particulate inside the filter wall was developed. A particulate cake layer filtration model which describes particle filtration in terms of more fundamental parameters was developed and coupled to the wall oxidation model. To better model the particulate oxidation kinetics, a model to take into account the NO2 produced in the washcoat of the CPF was developed. The overall 1-D 2-layer model can be used to predict the pressure drop of the exhaust gas across the filter, the evolution of particulate mass inside the filter, the particulate mass oxidized, the filtration efficiency and the particle number distribution downstream of the CPF. The model was used to better understand the internal performance of the CCRT®, by determining the components of the total pressure drop across the filter, by classifying the total particulate matter in layer I, layer II, the filter wall, and by the means of oxidation i.e. by O2, NO2 entering the filter and by NO2 being produced in the filter. The CPF model was calibrated at four temperatures in the range of 280 – 465 °C, and exhaust volumetric flow rates of 0.447 – 0.843 act-m3/sec, in CPF-only and CCRT ® (DOC+CPF) configurations. The clean filter wall permeability was determined to be 2.00E-13 m2, which is in agreement with values in the literature for cordierite filters. The particulate packing density in the filter wall had values between 2.92 kg/m3 - 3.95 kg/m3 for all the loads. The mean pore size of the catalyst loaded filter wall was found to be 11.0 µm. The particulate cake packing densities and permeabilities, ranged from 131 kg/m3 - 134 kg/m3, and 0.42E-14 m2 and 2.00E-14 m2 respectively, and are in agreement with the Peclet number correlations in the literature. Particulate cake layer porosities determined from the particulate cake layer filtration model ranged between 0.841 and 0.814 and decreased with load, which is about 0.1 lower than experimental and more complex discrete particle simulations in the literature. The thickness of layer I was kept constant at 20 µm. The model kinetics in the CPF-only and CCRT ® configurations, showed that no ’catalyst effect’ with O2 was present. The kinetic parameters for the NO2-assisted oxidation of particulate in the CPF were determined from the simulation of transient temperature programmed oxidation data in the literature. It was determined that the thermal and NO2 kinetic parameters do not change with temperature, exhaust flow rate or NO2 concentrations. However, different kinetic parameters are used for particulate oxidation in the wall and on the wall. Model results showed that oxidation of particulate in the pores of the filter wall can cause disproportionate decreases in the filter pressure drop with respect to particulate mass. The wall oxidation model along with the particulate cake filtration model were developed to model the sudden and rapid decreases in pressure drop across the CPF. The particulate cake and wall filtration models result in higher particulate filtration efficiencies than with just the wall filtration model, with overall filtration efficiencies of 98-99% being predicted by the model. The pre-exponential factors for oxidation by NO2 did not change with temperature or NO2 concentrations because of the NO2 wall production model. In both CPF-only and CCRT ® configurations, the model showed NO2 and layer I to be the dominant means and dominant physical location of particulate oxidation respectively. However, at temperatures of 280 °C, NO2 is not a significant oxidizer of particulate matter, which is in agreement with studies in the literature. The model showed that 8.6 and 81.6% of the CPF-inlet particulate matter was oxidized after 5 hours at 20 and 75% load in CCRT® configuration. In CPF-only configuration at the same loads, the model showed that after 5 hours, 4.4 and 64.8% of the inlet particulate matter was oxidized. The increase in NO2 concentrations across the DOC contributes significantly to the oxidation of particulate in the CPF and is supplemented by the oxidation of NO to NO2 by the catalyst in the CPF, which increases the particulate oxidation rates. From the model, it was determined that the catalyst in the CPF modeslty increases the particulate oxidation rates in the range of 4.5 – 8.3% in the CCRT® configuration. Hence, the catalyst loading in the CPF of the CCRT® could possibly be reduced without significantly decreasing particulate oxidation rates leading to catalyst cost savings and better engine performance due to lower exhaust backpressures.

Optical imaging of postsynaptic odor representation in the glomerular layer of the mouse olfactory bulb.

Olfactory glomeruli are the loci where the first odor-representation map emerges. The glomerular layer comprises exquisite local synaptic circuits for the processing of olfactory coding patterns immediately after their emergence. To understand how an odor map is transferred from afferent terminals to postsynaptic dendrites, it is essential to directly monitor the odor-evoked glomerular postsynaptic activity patterns. Here we report the use of a transgenic mouse expressing a Ca(2+)-sensitive green fluorescence protein (GCaMP2) under a Kv3.1 potassium-channel promoter. Immunostaining revealed that GCaMP2 was specifically expressed in mitral and tufted cells and a subpopulation of juxtaglomerular cells but not in olfactory nerve terminals. Both in vitro and in vivo imaging combined with glutamate receptor pharmacology confirmed that odor maps reported by GCaMP2 were of a postsynaptic origin. These mice thus provided an unprecedented opportunity to analyze the spatial activity pattern reflecting purely postsynaptic olfactory codes. The odor-evoked GCaMP2 signal had both focal and diffuse spatial components. The focalized hot spots corresponded to individually activated glomeruli. In GCaMP2-reported postsynaptic odor maps, different odorants activated distinct but overlapping sets of glomeruli. Increasing odor concentration increased both individual glomerular response amplitude and the total number of activated glomeruli. Furthermore, the GCaMP2 response displayed a fast time course that enabled us to analyze the temporal dynamics of odor maps over consecutive sniff cycles. In summary, with cell-specific targeting of a genetically encoded Ca(2+) indicator, we have successfully isolated and characterized an intermediate level of odor representation between olfactory nerve input and principal mitral/tufted cell output.

Simulating Cortical Development as a Self Constructing Process: A Novel Multi-Scale Approach Combining Molecular and Physical Aspects

Current models of embryological development focus on intracellular processes such as gene expression and protein networks, rather than on the complex relationship between subcellular processes and the collective cellular organization these processes support. We have explored this collective behavior in the context of neocortical development, by modeling the expansion of a small number of progenitor cells into a laminated cortex with layer and cell type specific projections. The developmental process is steered by a formal language analogous to genomic instructions, and takes place in a physically realistic three-dimensional environment. A common genome inserted into individual cells control their individual behaviors, and thereby gives rise to collective developmental sequences in a biologically plausible manner. The simulation begins with a single progenitor cell containing the artificial genome. This progenitor then gives rise through a lineage of offspring to distinct populations of neuronal precursors that migrate to form the cortical laminae. The precursors differentiate by extending dendrites and axons, which reproduce the experimentally determined branching patterns of a number of different neuronal cell types observed in the cat visual cortex. This result is the first comprehensive demonstration of the principles of self-construction whereby the cortical architecture develops. In addition, our model makes several testable predictions concerning cell migration and branching mechanisms.