Fluorescence Microscopy Imaging Denoising with Log-Euclidean Priors and Photobleaching Compensation

Fluorescent protein microscopy imaging is nowadays one of the most important tools in biomedical research. However, the resulting images present a low signal to noise ratio and a time intensity decay due to the photobleaching effect. This phenomenon is a consequence of the decreasing on the radiation emission efficiency of the tagging protein. This occurs because the fluorophore permanently loses its ability to fluoresce, due to photochemical reactions induced by the incident light. The Poisson multiplicative noise that corrupts these images, in addition with its quality degradation due to photobleaching, make long time biological observation processes very difficult. In this paper a denoising algorithm for Poisson data, where the photobleaching effect is explicitly taken into account, is described. The algorithm is designed in a Bayesian framework where the data fidelity term models the Poisson noise generation process as well as the exponential intensity decay caused by the photobleaching. The prior term is conceived with Gibbs priors and log-Euclidean potential functions, suitable to cope with the positivity constrained nature of the parameters to be estimated. Monte Carlo tests with synthetic data are presented to characterize the performance of the algorithm. One example with real data is included to illustrate its application.

Solubility of Ethene in Water and in a Medium for the Cultivation of a Bacterial Strain

The solubility of ethene in water and in the fermentation medium of Xanthobacter Py(2) was determined with a Ben-Naim-Baer type apparatus. The solubility measurements were carried out in the temperature range of (293.15 to 323.15) K and at atmospheric pressure with a precision of about +/- 0.3 %. The Ostwald coefficients, the mole fractions of the dissolved ethene, at the gas partial pressure of 101.325 kPa, and the Henry coefficients, at the water vapor pressure, were calculated using accurate thermodynamic relations. A comparison between the solubility of ethene in water and in the cultivation medium has shown that this gas is about 2.4 % more soluble in pure water. On the other hand, from the solubility temperature dependence, the Gibbs energy, enthalpy, and entropy changes for the process of transferring the solute from the gaseous phase to the liquid solutions were also determined. Moreover, the perturbed-chain statistical associating fluid theory equation of state (PC-SAFT EOS) model was used for the prediction of the solubility of ethene in water. New parameters, k(ij), are proposed for this system, and it was found that using a ky temperature-dependent PC-SAFT EOS describes more accurately the behavior solubilities of ethene in water at 101.325 kPa, improving the deviations to 1 %.

Trends in properties of para-substituted 3-(phenylhydrazo)pentane-2,4-diones

Trends between the Hammett's sigma(p) and related normal sigma(n)(p), inductive sigma(I), resonance sigma(R), negative sigma(-)(p) and positive sigma(+)(p) polar conjugation and Taft's sigma(o)(p) substituent constants and the N-H center dot center dot center dot O distance, delta(N-H) NMR chemical shift, oxidation potential (E-p/2(ox), measured in this study by cyclic voltammetry (CV)) and thermodynamic parameters (pK, Delta G(0), Delta H-0 and Delta S-0) of the dissociation process of unsubstituted 3-(phenylhydrazo)pentane-2,4-dione (HL1) and its para-substituted chloro (HL2), carboxy (HL3), fluoro (HL4) and nitro (HL5) derivatives were recognized. The best fits were found for sigma(p) and/or sigma(-)(p) in the cases of d(N center dot center dot center dot O), delta(N-H) and E-p/2(ox), showing the importance of resonance and conjugation effects in such properties, whereas for the above thermodynamic properties the inductive effects (sigma(I)) are dominant. HL2 exists in the hydrazo form in DMSO solution and in the solid state and contains an intramolecular H-bond with the N center dot center dot center dot O distance of 2.588(3)angstrom. It was also established that the dissociation process of HL1-5 is non-spontaneous, endothermic and entropically unfavourable, and that the increase in the inductive effect (sigma(I)) of para-substitutents (-H < -Cl < -COOH < -F < -NO2) leads to the corresponding growth of the N center dot center dot center dot O distance and decrease of the pK and of the changes of Gibbs free energy, of enthalpy and of entropy for the HL1-5 acid dissociation process. The electrochemical behaviour of HL1-5 was interpreted using theoretical calculations at the DFT/HF hybrid level, namely in terms of HOMO and LUMO compositions, and of reactivities induced by anodic and cathodic electron-transfers. Copyright (C) 2010 John Wiley & Sons, Ltd.

Impact of maritime air mass trajectories on the Western European coast urban aerosol

Lisbon is the largest urban area in the Western European coast. Due to this geographical position the Atlantic Ocean serves as an important source of particles and plays an important role in many atmospheric processes. The main objectives of this study were to (1) perform a chemical characterization of particulate matter (PM2.5) sampled in Lisbon, (2) identify the main sources of particles, (3) determine PM contribution to this urban area, and (4) assess the impact of maritime air mass trajectories on concentration and composition of respirable PM sampled in Lisbon. During 2007, PM2.5 was collected on a daily basis in the center of Lisbon with a Partisol sampler. The exposed Teflon filters were measured by gravimetry and cut into two parts: one for analysis by instrumental neutron activation analysis (INAA) and the other by ion chromatography (IC). Principal component analysis (PCA) and multilinear regression analysis (MLRA) were used to identify possible sources of PM2.5 and determine mass contribution. Five main groups of sources were identified: secondary aerosols, traffic, calcium, soil, and sea. Four-day backtracking trajectories ending in Lisbon at the starting sampling time were calculated using the HYSPLIT model. Results showed that maritime transport scenarios were frequent. These episodes were characterized by a significant decrease of anthropogenic aerosol concentrations and exerted a significant role on air quality in this urban area.

Impact of Sahara dust transport on Cape Verde atmospheric element particles

The objectives of this study were to (1) conduct an elemental characterization of airborne particles sampled in Cape Verde and (2) assess the influence of Sahara desert on local suspended particles. Particulate matter (PM10) was collected in Praia city (14°94'N; 23°49'W) with a low-volume sampler in order to characterize its chemical composition by k0-INAA. The filter samples were first weighed and subsequently irradiated at the Portuguese Research Reactor. Results showed that PM10 concentrations in Cape Verde markedly exceeded the health-based air quality standards defined by the European Union (EU), World Health Organization (WHO), and U.S. Environmental Protection Agency (EPA), in part due to the influence of Sahara dust transport. The PM10 composition was characterized essentially by high concentrations of elements originating from the soil (K, Sm, Co, Fe, Sc, Rb, Cr, Ce, and Ba) and sea (Na), and low concentrations of anthropogenic elements (As, Zn, and Sb). In addition, the high concentrations of PM measured in Cape Verde suggest that health of the population may be less affected compared with other sites where PM10 concentrations are lower but more enriched with toxic elements.

Accessing indoor fungal contamination using conventional and molecular methods in Portuguese poultries

Epidemiological studies showed increased prevalence of respiratory symptoms and adverse changes in pulmonary function parameters in poultry workers, corroborating the increased exposure to risk factors, such as fungal load and their metabolites. This study aimed to determine the occupational exposure threat due to fungal contamination caused by the toxigenic isolates belonging to the complex of the species of Aspergillus flavus and also isolates fromAspergillus fumigatus species complex. The study was carried out in seven Portuguese poultries, using cultural and molecularmethodologies. For conventional/cultural methods, air, surfaces, and litter samples were collected by impaction method using the Millipore Air Sampler. For the molecular analysis, air samples were collected by impinger method using the Coriolis μ air sampler. After DNA extraction, samples were analyzed by real-time PCR using specific primers and probes for toxigenic strains of the Aspergillus flavus complex and for detection of isolates from Aspergillus fumigatus complex. Through conventional methods, and among the Aspergillus genus, different prevalences were detected regarding the presence of Aspergillus flavus and Aspergillus fumigatus species complexes, namely: 74.5 versus 1.0% in the air samples, 24.0 versus 16.0% in the surfaces, 0 versus 32.6% in new litter, and 9.9 versus 15.9%in used litter. Through molecular biology, we were able to detect the presence of aflatoxigenic strains in pavilions in which Aspergillus flavus did not grow in culture. Aspergillus fumigatus was only found in one indoor air sample by conventional methods. Using molecular methodologies, however, Aspergillus fumigatus complex was detected in seven indoor samples from three different poultry units. The characterization of fungal contamination caused by Aspergillus flavus and Aspergillus fumigatus raises the concern of occupational threat not only due to the detected fungal load but also because of the toxigenic potential of these species.

Occupational exposure to toxigenic fungi from Aspergillus flavus complex

Bioaerosols are mainly composed of fungal particles, bacteria and plant spores, being fungi responsible for the release of VOCs and micotoxins into indoor environments. Aspergillus flavus is a common opportunistic pathogen causing human infections and is involved in the production of aflatoxin and other secondary metabolites associated with toxic and allergic reactions. Poultry workers are exposed to high concentrations of fungi and are therefore more prone to develop associated pathologies. To evaluate occupational exposure of the workers to Aspergillus flavus and aflatoxins, six animal production facilities were selected, including 10 buildings, from which indoor air samples and outdoor reference samples were obtained. Twenty-five duplicate samples were collected by two methodologies: impactation onto malt extract agar of 25L air samples using a Millipore Air Tester were used to evaluate quantitative (CFU/m3) and qualitative (species identification, whenever possible) sample composition; 300 L air samples collected with the Coriolis Air Sampler into phosphate–saline buffer were used to isolate DNA, following molecular identification of Aspergillus section flavi using nor-1 specific primers by real-time PCR.

Fungal contamination in two Portuguese wastewater treatment plants

The presence of filamentous fungi was detected in wastewater and air collected at wastewater treatment plants (WWTP) from several European countries. The aim of the present study was to assess fungal contamination in two WWTP operating in Lisbon. In addition, particulate matter (PM) contamination data was analyzed. To apply conventional methods, air samples from the two plants were collected through impaction using an air sampler with a velocity air rate of 140 L/min. Surfaces samples were collected by swabbing the surfaces of the same indoor sites. All collected samples were incubated at 27°C for 5 to 7 d. After lab processing and incubation of collected samples, quantitative and qualitative results were obtained with identification of the isolated fungal species. For molecular methods, air samples of 250 L were also collected using the impinger method at 300 L/min airflow rate. Samples were collected into 10 ml sterile phosphate-buffered saline with 0.05% Triton X-100, and the collection liquid was subsequently used for DNA extraction. Molecular identification of Aspergillus fumigatus and Stachybotrys chartarum was achieved by real-time polymerase chain reaction (RT-PCR) using the Rotor-Gene 6000 qPCR Detection System (Corbett). Assessment of PM was also conducted with portable direct-reading equipment (Lighthouse, model 3016 IAQ). Particles concentration measurement was performed at five different sizes: PM0.5, PM1, PM2.5, PM5, and PM10. Sixteen different fungal species were detected in indoor air in a total of 5400 isolates in both plants. Penicillium sp. was the most frequently isolated fungal genus (58.9%), followed by Aspergillus sp. (21.2%) and Acremonium sp. (8.2%), in the total underground area. In a partially underground plant, Penicillium sp. (39.5%) was also the most frequently isolated, also followed by Aspergillus sp. (38.7%) and Acremonium sp. (9.7%). Using RT-PCR, only A. fumigatus was detected in air samples collected, and only from partial underground plant. Stachybotrys chartarum was not detected in any of the samples analyzed. The distribution of particle sizes showed the same tendency in both plants; however, the partially underground plant presented higher levels of contamination, except for PM2.5. Fungal contamination assessment is crucial to evaluating the potential health risks to exposed workers in these settings. In order to achieve an evaluation of potential health risks to exposed workers, it is essential to combine conventional and molecular methods for fungal detection. Protective measures to minimize worker exposure to fungi need to be adopted since wastewater is the predominant internal fungal source in this setting.

Potential poultry and meat products contamination by aflatoxin B1 due to fungal presence in Portuguese poultry units

The impact of mycotoxins on human and animal health is well recognized. Aflatoxin B1 (AFB1) is by far the most prevalent and the most potent natural carcinogen and is usually the major aflatoxin produced by toxigenic fungal strains. Data available, points to an increasing frequency of poultry feed contamination by aflatoxins. Since aflatoxin residues may accumulate in body tissues, this represents a high risk to human health. Samples from commercial poultry birds have already presented detectable levels of aflatoxin in liver. A descriptive study was developed in order to assess fungal contamination by species from Aspergillus flavus complex in seven Portuguese poultry units. Air fungal contamination was studied by conventional and molecular methods. Air, litter and surfaces samples were collected. To apply molecular methods, air samples of 300L were collected using the Coriolis μ air sampler (Bertin Technologies), at 300 L/min airflow rate. For conventional methodologies, all the collected samples were incubated at 27ºC for five to seven days. Through conventional methods, Aspergillus flavus was the third fungal species (7%) most frequently found in 27 indoor air samples analysed and the most commonly isolated species (75%) in air samples containing only the Aspergillus genus...

Fungal burden in waste industry: an occupational risk to be solved

High loads of fungi have been reported in different types of waste management plants. This study intends to assess fungal contamination in one waste-sorting plant before and after cleaning procedures in order to analyze their effectiveness. Air samples of 50 L were collected through an impaction method, while surface samples, taken at the same time, were collected by the swabbing method and subject to further macro- and microscopic observations. In addition, we collected air samples of 250 L using the impinger Coriolis μ air sampler (Bertin Technologies) at 300 L/min airflow rate in order to perform real-time quantitative PCR (qPCR) amplification of genes from specific fungal species, namely Aspergillus fumigatus and Aspergillus flavus complexes, as well as Stachybotrys chartarum species. Fungal quantification in the air ranged from 180 to 5,280 CFU m−3 before cleaning and from 220 to 2,460 CFU m−3 after cleaning procedures. Surfaces presented results that ranged from 29 × 104 to 109 × 104 CFU m−2 before cleaning and from 11 × 104 to 89 × 104 CFU m−2 after cleaning. Statistically significant differences regarding fungal load were not detected between before and after cleaning procedures. Toxigenic strains from A. flavus complex and S. chartarum were not detected by qPCR. Conversely, the A. fumigatus species was successfully detected by qPCR and interestingly it was amplified in two samples where no detection by conventional methods was observed. Overall, these results reveal the inefficacy of the cleaning procedures and that it is important to determine fungal burden in order to carry out risk assessment.

Characterizing the fungal and bacterial microflora and concentrations in fitness centres

Fitness centres are special places where conditions for microbiological proliferation should be considered. Moisture due to human perspiration and water condensation as a result of human physical activities are prevalent in this type of buildings. Exposure to microbial contaminants is clinically associated with respiratory disorders and people who work out in polluted environments would be susceptible to contaminants. This work studied the indoor air contamination in three gymnasiums in Lisbon. The sampling was performed at two periods: at the opening (morning) and closing (night) of the three gymnasiums. The airborne bacterial and fungal populations were sampled by impaction directly onto Tryptic Soy Agar (for bacteria) and Malt Extract Agar (for fungi) plates, using a Merck MAS-100 air sampler. Higher bacterial concentrations were found at night as compared to the morning but the same behaviour was not found for fungal concentrations. Gram-negative catalase positive cocci were the dominant bacteria in indoor air samples of the studied gymnasiums. In this study, 21 genera/species of fungal colonies were identified. Chrysosporium sp., Chrysonilia sp., Neoscytalidium hialinum, Sepedonium sp. and Penicillium sp. were the most prevalent species identified in the morning, while Cladosporium sp., Penicillium sp., Chrysosporium sp., Acremonium sp. and Chrysonilia sp. were more prevalent at night. A well-designed sanitation and maintenance program for gymnasiums is needed to ensure healthier space for indoor physical activity.