Quantitative optical coherence tomography for characterization of microscopic structures with varying refractive index

In this paper we have done back to back comparison of quantitive phase and refractive index from a microscopic image of waveguide previously obtained by Allsop et al. Paper also shows microscopic image of the first 3 waveguides from the sample. Tomlins et al. have demonstrated use of femtosecond fabricated artefacts as OCT calibration samples. Here we present the use of femtosecond waveguides, inscribed with optimized parameters, to test and calibrate the sensitivity of the OCT systems.

Comprehensive characterization of snowfall in terms of microphysical features, quantitative precipitation estimation and scavenging properties by in situ and remote sensing observations at an Antarctic coastal site

Snow plays a crucial role in the Earth's hydrological cycle and energy budget, making its monitoring necessary. In this context, ground-based radars and in situ instruments are essential thanks to their spatial coverage, resolution, and temporal sampling. Deep understanding and reliable measurements of snow properties are crucial over Antarctica to assess potential future changes of the surface mass balance (SMB) and define the contribution of the Antarctic ice sheet on sea-level rise. However, despite its key role, Antarctic precipitation is poorly investigated due to the continent's inaccessibility and extreme environment. In this framework, this Thesis aims to contribute to filling this gap by in-depth characterization of Antarctic precipitation at the Mario Zucchelli station from different points of view: microphysical features, quantitative precipitation estimation (QPE), vertical structure of precipitation, and scavenging properties. For this purpose, a K-band vertically pointing radar collocated with a laser disdrometer and an optical particle counter (OPC) were used. The radar probed the lowest atmospheric layers with high vertical resolution, allowing the first trusted measurement at only 105 m height. Disdrometer and OPC provided information on the particle size distribution and aerosol concentrations. An innovative snow classification methodology was designed by comparing the radar reflectivity (Ze) and disdrometer-derived reflectivity by means of DDA simulations. Results of classification were exploited in QPE through appropriate Ze-snow rate relationships. The accuracy of the resulting QPE was benchmarked against a collocated weighing gauge. Vertical radar profiles were also investigated to highlight hydrometeors' sublimation and growth processes. Finally, OPC and disdrometer data allowed providing the first-ever estimates of scavenging properties of Antarctic snowfall. Results presented in this Thesis give rise to advances in knowledge of the characteristics of snowfall in Antarctica, contributing to a better assessment of the SMB of the Antarctic ice sheet, the major player in the global sea-level rise.

Mineralogical characterization of a highly-weathered soil by the Rietveld Method

The mineralogical characterization through mineral quantification of Brazilian soils by X-ray diffraction data using the Rietveld Method is not common. A mineralogical quantification of an Acric Ferralsol from the Ponta Grossa region, state of Paraná, Brazil, was carried out using this Method with X-Ray Diffraction data to verify if this method was suitable for mineral quantification of a highly-weathered soil. The A, AB and B3 horizons were fractioned to separate the different particle sizes: clay, silt, fine sand (by Stokes Law) and coarse sand fractions (by sieving), with the procedure free of chemical treatments. X-ray Fluorescence, Inductively Coupled Plasma Atomic Emission Spectrometry, Infrared Spectroscopy and Mössbauer Spectroscopy were used in order to assist the mineral identification and quantification. The Rietveld Method enabled the quantification of the present minerals. In a general way, the quantitative mineralogical characterization by the Rietveld Method revealed that quartz, gibbsite, rutile, hematite, goethite, kaolinite and halloysite were present in the clay and silt fractions of all horizons. The silt fractions of the deeper horizons were different from the more superficial ones due to the presence of large amounts of quartz. The fine and the coarse sand fractions are constituted mainly by quartz. Therefore, a mineralogical quantification of the finer fraction (clay and silt) by the Rietveld Method was successful.

An overview of the Amazonian Aerosol Characterization Experiment 2008 (AMAZE-08)

The Amazon Basin provides an excellent environment for studying the sources, transformations, and properties of natural aerosol particles and the resulting links between biological processes and climate. With this framework in mind, the Amazonian Aerosol Characterization Experiment (AMAZE-08), carried out from 7 February to 14 March 2008 during the wet season in the central Amazon Basin, sought to understand the formation, transformations, and cloud-forming properties of fine-and coarse-mode biogenic aerosol particles, especially as related to their effects on cloud activation and regional climate. Special foci included (1) the production mechanisms of secondary organic components at a pristine continental site, including the factors regulating their temporal variability, and (2) predicting and understanding the cloud-forming properties of biogenic particles at such a site. In this overview paper, the field site and the instrumentation employed during the campaign are introduced. Observations and findings are reported, including the large-scale context for the campaign, especially as provided by satellite observations. New findings presented include: (i) a particle number-diameter distribution from 10 nm to 10 mu m that is representative of the pristine tropical rain forest and recommended for model use; (ii) the absence of substantial quantities of primary biological particles in the submicron mode as evidenced by mass spectral characterization; (iii) the large-scale production of secondary organic material; (iv) insights into the chemical and physical properties of the particles as revealed by thermodenuder-induced changes in the particle number-diameter distributions and mass spectra; and (v) comparisons of ground-based predictions and satellite-based observations of hydrometeor phase in clouds. A main finding of AMAZE-08 is the dominance of secondary organic material as particle components. The results presented here provide mechanistic insight and quantitative parameters that can serve to increase the accuracy of models of the formation, transformations, and cloud-forming properties of biogenic natural aerosol particles, especially as related to their effects on cloud activation and regional climate.

Characterization of Yeast Extracellular Vesicles: Evidence for the Participation of Different Pathways of Cellular Traffic in Vesicle Biogenesis

Background: Extracellular vesicles in yeast cells are involved in the molecular traffic across the cell wall. In yeast pathogens, these vesicles have been implicated in the transport of proteins, lipids, polysaccharide and pigments to the extracellular space. Cellular pathways required for the biogenesis of yeast extracellular vesicles are largely unknown. Methodology/Principal Findings: We characterized extracellular vesicle production in wild type (WT) and mutant strains of the model yeast Saccharomyces cerevisiae using transmission electron microscopy in combination with light scattering analysis, lipid extraction and proteomics. WT cells and mutants with defective expression of Sec4p, a secretory vesicle-associated Rab GTPase essential for Golgi-derived exocytosis, or Snf7p, which is involved in multivesicular body (MVB) formation, were analyzed in parallel. Bilayered vesicles with diameters at the 100-300 nm range were found in extracellular fractions from yeast cultures. Proteomic analysis of vesicular fractions from the cells aforementioned and additional mutants with defects in conventional secretion pathways (sec1-1, fusion of Golgi-derived exocytic vesicles with the plasma membrane; bos1-1, vesicle targeting to the Golgi complex) or MVB functionality (vps23, late endosomal trafficking) revealed a complex and interrelated protein collection. Semi-quantitative analysis of protein abundance revealed that mutations in both MVB- and Golgi-derived pathways affected the composition of yeast extracellular vesicles, but none abrogated vesicle production. Lipid analysis revealed that mutants with defects in Golgi-related components of the secretory pathway had slower vesicle release kinetics, as inferred from intracellular accumulation of sterols and reduced detection of these lipids in vesicle fractions in comparison with WT cells. Conclusions/Significance: Our results suggest that both conventional and unconventional pathways of secretion are required for biogenesis of extracellular vesicles, which demonstrate the complexity of this process in the biology of yeast cells.

Characterization of different fruit wines made from cacao, cupuassu, gabiroba, jaboticaba and umbu

The main aim of this work was to produce fruit wines from pulp of gabiroba, cacao, umbu, cupuassu and jaboticaba and characterize them using gas chromatography-mass spectrometry for determination of minor compounds and gas chromatography-flame ionization detection for major compounds. Ninety-nine compounds (C(6) compounds, alcohols, monoterpenic alcohols, monoterpenic oxides, ethyl esters, acetates, volatile phenols, acids, carbonyl compounds, sulfur compounds and sugars) were identified in fruit wines. The typical composition for each fruit wine was evidenced by principal component analysis and Tukey test. The yeast UFLA CA 1162 was efficient in the fermentation of the fruit pulp used in this work. The identification and quantification of the compounds allowed a good characterization of the fruit wines. With our results, we conclude that the use of tropical fruits in the production of fruit wines is a viable alternative that allows the use of harvest surpluses and other underused fruits, resulting in the introduction of new products into the market. (C) 2010 Elsevier Ltd. All rights reserved.

Cluster identification and characterization in the riser of a circulating fluidized bed from numerical simulation results

A methodology of identification and characterization of coherent structures mostly known as clusters is applied to hydrodynamic results of numerical simulation generated for the riser of a circulating fluidized bed. The numerical simulation is performed using the MICEFLOW code, which includes the two-fluids IIT`s hydrodynamic model B. The methodology for cluster characterization that is used is based in the determination of four characteristics, related to average life time, average volumetric fraction of solid, existing time fraction and frequency of occurrence. The identification of clusters is performed by applying a criterion related to the time average value of the volumetric solid fraction. A qualitative rather than quantitative analysis is performed mainly owing to the unavailability of operational data used in the considered experiments. Concerning qualitative analysis, the simulation results are in good agreement with literature. Some quantitative comparisons between predictions and experiment were also presented to emphasize the capability of the modeling procedure regarding the analysis of macroscopic scale coherent structures. (c) 2007 Elsevier Inc. All rights reserved.

Chemical-mineralogical characterization of C&D waste recycled aggregates from Sao Paulo, Brazil

This study presents a methodology for the characterization of construction and demolition (C&D) waste recycled aggregates based on a combination of analytical techniques (X-ray fluorescence (XRF), soluble ions, semi-quantitative X-ray diffraction (XRD), thermogravimetric analysis (TCA-DTG) and hydrochloric acid (HCl) selective dissolution). These combined analytical techniques allow for the estimation of the amount of cement paste, its most important hydrated and carbonated phases, as well as the amount of clay and micas. Details of the methodology are presented here and the results of three representative C&D samples taken from the Sao Paulo region in Brazil are discussed. Chemical compositions of mixed C&D aggregate samples have mostly been influenced by particle size rather than the visual classification of C&D into red or grey and geographical origin. The amount of measured soluble salts in C&D aggregates (0.15-25.4 mm) is lower than the usual limits for mortar and concrete production. The content of porous cement paste in the C&D aggregates is around 19.3% (w/w). However, this content is significantly lower than the 43% detected for the C&D powders (< 0.15 min). The clay content of the powders was also high, potentially resulting from soil intermixed with the C&D waste, as well as poorly burnt red ceramic. Since only about 50% of the measured CaO is combined with CO(2), the powders have potential use as raw materials for the cement industry. (C) 2008 Elsevier Ltd. All rights reserved.

Characterization of peroxisome proliferator-activated receptor alpha in normal rat mammary gland and 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine-induced mammary gland tumors from rats fed high and low fat diets

Normal Sprague-Dau ley rat mammary gland epithelial cells and mammary gland carcinomas induced by 2-amino-1 -methyl-6-phenylimidazo[4,5-b]pyridine, a carcinogen found in the diet, were examined for the expression of peroxisome proliferator-activated receptor alpha (PPAR alpha). PPAR alpha mRNA and protein was detected in normal and tumor tissue by reverse transcriptase polymerase chain reaction (RT-PCR) and immunohistochemistry. By quantitative RT-PCR, carcinomas had a 12-fold higher expression than control mammary glands, a statistically significant difference. PPAR alpha expression was examined in carcinomas and normal tissues from rats on high fat (23.5/% corn oil) and low fat (5% corn oil) diets. Although neither carcinomas, nor control tissues showed statistically significant differences between the two diet groups, PPAR alpha expression was the highest in carcinomas from rats on the high fat diet. The expression of PPAR alpha in normal mammary gland and its significant elevation in mammary gland carcinomas raises the possibility of its involvement in mammary gland physiology and pathophysiology. (C) 2000 Published by Elsevier Science Ireland Ltd. All rights reserved.

Characterization of Adherent Umbilical Cord Blood Stromal Cells Regarding Passage, Cell Number, and Nano-biomarking Utilization

Adherent umbilical cord blood stromal cells (AUCBSCs) are multipotent cells with differentiation capacities. Therefore, these cells have been investigated for their potential in cell-based therapies. Quantum Dots (QDs) are an alternative to organic dyes and fluorescent proteins because of their long-term photostability. In this study we determined the effects of the cell passage on AUCBSCs morphology, phenotype, and differentiation potential. QDs labeled AUCBSCs in the fourth cell passage were differentiated in the three mesodermal lineages and were evaluated using cytochemical methods and transmission electron microscopy (TEM). Gene and protein expression of the AUCBSCs immunophenotypic markers were also evaluated in the labeled cells by real-time quantitative PCR and flow cytometry. In this study we were able to define the best cellular passage to work with AUCBSCs and we also demonstrated that the use of fluorescent QDs can be an efficient nano-biotechnological tool in differentiation studies because labeled cells do not have their characteristics compromised.

Characterization of acid-base status in maintenance hemodialysis: physicochemical approach

Acidosis is a common and deleterious aspect of maintenance dialysis. Traditionally, it is considered to be an elevated anion gap acidosis caused by the inability to excrete nonvolatile anions. Stewart`s approach made it possible to identify real determinants of the acid-base status and allowed quantification of the components of these disturbances, especially the unmeasured anions. We performed a cross-sectional study to identify and quantify each component of acidosis in hemodialysis maintenance patients. Sixty-four maintenance hemodialysis patients and 14 controls were enrolled in this study. Gasometrical and biochemical analysis were performed before the midweek dialysis session. Quantitative physicochemical analysis was carried out using the Stewart methodology. Hemodialysis patients were found to have mild acidemia (mean pH: 7.33 +/- 0.06 versus 7.41 +/- 0.05) secondary to metabolic acidosis (serum bicarbonate: 18.8 +/- 0.26 versus 25.2 +/- 0.48 mEq/l). The metabolic acidosis was due to retention of unmeasured anions (6.5 +/- 0.29 versus 3.1 +/- 0.62 mEq/l), hyperchloremia (105.1 +/- 0.5 versus 101.8 +/- 0.7 mEq/l), and hyperphosphatemia (5.90 +/- 0.19 versus 3.66 +/- 0.14 mg/dl). Compared with control values, the unmeasured anions and hyperchloremia had a similar acidifying effect (3.4 and 3.3 mEq/l), corresponding to almost 90% of the metabolic acidosis. Unmeasured anions and hyperchloremia are important components of acidosis in maintenance hemodialysis, in addition to phosphorus. Future studies to determine the etiology and consequences of hyperchloremic acidosis are warranted.

In vivo electrochemical characterization and inflammatory response of multiwalled carbon nanotube-based electrodes in rat hippocampus

Stimulating neural electrodes are required to deliver charge to an environment that presents itself as hostile. The electrodes need to maintain their electrical characteristics (charge and impedance) in vivo for a proper functioning of neural prostheses. Here we design implantable multi-walled carbon nanotubes coating for stainless steel substrate electrodes, targeted at wide frequency stimulation of deep brain structures. In well-controlled, low-frequency stimulation acute experiments, we show that multi-walled carbon nanotube electrodes maintain their charge storage capacity (CSC) and impedance in vivo. The difference in average CSCs (n = 4) between the in vivo (1.111 mC cm(-2)) and in vitro (1.008 mC cm(-2)) model was statistically insignificant (p > 0.05 or P-value = 0.715, two tailed). We also report on the transcription levels of the pro-inflammatory cytokine IL-1 beta and TLR2 receptor as an immediate response to low-frequency stimulation using RT-PCR. We show here that the IL-1 beta is part of the inflammatory response to low-frequency stimulation, but TLR2 is not significantly increased in stimulated tissue when compared to controls. The early stages of neuroinflammation due to mechanical and electrical trauma induced by implants can be better understood by detection of pro-inflammatory molecules rather than by histological studies. Tracking of such quantitative response profits from better analysis methods over several temporal and spatial scales. Our results concerning the evaluation of such inflammatory molecules revealed that transcripts for the cytokine IL-1 beta are upregulated in response to low-frequency stimulation, whereas no modulation was observed for TLR2. This result indicates that the early response of the brain to mechanical trauma and low-frequency stimulation activates the IL-1 beta signaling cascade but not that of TLR2.

Biophysical characterization of interactions involving importin-alpha during nuclear import

Proteins containing the classical nuclear localization sequences (NLSs) are imported into the nucleus by the importin-alpha/beta heterodimer. Importin-alpha contains the NLS binding site, whereas importin-beta mediates the translocation through the nuclear pore. We characterized the interactions involving importin-alpha during nuclear import using a combination of biophysical techniques (biosensor, crystallography, sedimentation equilibrium, electrophoresis, and circular dichroism). Importin-alpha is shown to exist in a monomeric autoinhibited state (association with NLSs undetectable by biosensor). Association with importin-beta (stoichiometry, 1:1; K-D = 1.1 x 10(-8) m) increases the affinity for NLSs; the importin-alpha/beta complex binds representative monopartite NLS (simian virus 40 large T-antigen) and bipartite NLS (nucleoplasmin) with affinities (K-D = 3.5 x 10(-8) m and 4.8 x 10(-8) m, respectively) comparable with those of a truncated importin-alpha lacking the autoinhibitory domain (T-antigen NLS, K-D = 1.7 x 10(-8) m; nucleoplasmin NLS, K-D = 1.4 x 10(-8) m). The autoinhibitory domain (as a separate peptide) binds the truncated importin-alpha, and the crystal structure of the complex resembles the structure of full-length importin-alpha. Our results support the model of regulation of nuclear import mediated by the intrasteric autoregulatory sequence of importin-alpha and provide a quantitative description of the binding and regulatory steps during nuclear import.

The development of chromatography for the characterization of protein interactions: a personal perspective

This article reviews the progress of a personal endeavour to develop chromatography as a quantitative procedure for the determination of reaction stoichiometries and equilibrium constants governing protein interactions. As well as affording insight into an aspect of chromatography with which many protein chemists are unfamiliar, it shows the way in which minor adaptations of conventional chromatographic practices have rendered the technique one of the most powerful methods available for the characterization of interactions. That pathway towards quantification is followed from the introduction of frontal gel filtration for the study of protein self-association to the characterization of ligand binding by the biosensor variant of quantitative affinity chromatography.

Accessing Planktothrix species diversity and associated toxins using quantitative real-time PCR in natural waters

Tese de Doutoramento em Biologia apresentada à Faculdade de Ciências da Universidade do Porto, 2015.