Arrow Plot: a new graphical tool for selecting up and down regulated genes and genes differentially expressed on samples subgroups

Background: A common task in analyzing microarray data is to determine which genes are differentially expressed across two (or more) kind of tissue samples or samples submitted under experimental conditions. Several statistical methods have been proposed to accomplish this goal, generally based on measures of distance between classes. It is well known that biological samples are heterogeneous because of factors such as molecular subtypes or genetic background that are often unknown to the experimenter. For instance, in experiments which involve molecular classification of tumors it is important to identify significant subtypes of cancer. Bimodal or multimodal distributions often reflect the presence of subsamples mixtures. Consequently, there can be genes differentially expressed on sample subgroups which are missed if usual statistical approaches are used. In this paper we propose a new graphical tool which not only identifies genes with up and down regulations, but also genes with differential expression in different subclasses, that are usually missed if current statistical methods are used. This tool is based on two measures of distance between samples, namely the overlapping coefficient (OVL) between two densities and the area under the receiver operating characteristic (ROC) curve. The methodology proposed here was implemented in the open-source R software. Results: This method was applied to a publicly available dataset, as well as to a simulated dataset. We compared our results with the ones obtained using some of the standard methods for detecting differentially expressed genes, namely Welch t-statistic, fold change (FC), rank products (RP), average difference (AD), weighted average difference (WAD), moderated t-statistic (modT), intensity-based moderated t-statistic (ibmT), significance analysis of microarrays (samT) and area under the ROC curve (AUC). On both datasets all differentially expressed genes with bimodal or multimodal distributions were not selected by all standard selection procedures. We also compared our results with (i) area between ROC curve and rising area (ABCR) and (ii) the test for not proper ROC curves (TNRC). We found our methodology more comprehensive, because it detects both bimodal and multimodal distributions and different variances can be considered on both samples. Another advantage of our method is that we can analyze graphically the behavior of different kinds of differentially expressed genes. Conclusion: Our results indicate that the arrow plot represents a new flexible and useful tool for the analysis of gene expression profiles from microarrays.

HIV infection and AIDS in a small municipality in Southeast Brazil

OBJECTIVE: Studies on the aspects of HIV infection in small Brazilian municipalities are invaluable to appropriately design control strategies, better allocate resources, and improve health care services. The objective of the study was to assess the clinical and epidemiological aspects of HIV infection in a small municipality. METHODS: A descriptive study was carried out in Miracema, a small municipality in the northwestern area of the state of Rio de Janeiro, Brazil, between July 1999 and December 2003. All HIV-infected adult patients followed up at the local HIV/AIDS Program were included. Clinical and epidemiologic characteristics were prospectively assessed through standardized questionnaires. RESULTS: A total of 65 adult patients who attended the local HIV/AIDS Program were analyzed. Most (34) were women (male to female ratio: 0.9). An absolute predominance of patients who were born in Miracema or neighboring municipalities (94%), lived in Miracema (90.7%), were single (70.8%), attributed the acquisition of HIV infection to unprotected heterosexual intercourse (72.3%) and had a past history of snorting cocaine (27.7) was found Central nervous system disorders (including five cases of cryptococcal meningitis) and acute pulmonary pneumocystosis-like respiratory failure were major causes of morbidity. Most patients (56.9%) were at presented in advanced stages of HIV infection. CONCLUSIONS: The predominance of patients on advanced stages of HIV infection suggest the existence of a large pool of undiagnosed cases in the community. A major feature of the cohort was an inverted male to female ratio. Further investigations over a broader geographic area are urgently needed for better understanding the clinical and epidemiological characteristics of HIV infection in small Brazilian municipalities and rural areas.

Occupational exposure to aflatoxin B1: the case of poultry and swine production

Although there is an abundance of literature concerning the ingestion of food contaminated with aflatoxin B1 (AFB1), only a small number of studies explore mycotoxin exposure in occupational settings. Taking this into consideration, our study was developed with the intention of elucidating whether there is occupational exposure to AFB1 in Portuguese poultry and swine production facilities. A specific biomarker was used to assess exposure to AFB1. A total of 45 workers (34 from poultry farms; 11 from swine production facilities) participated in this study, providing blood samples. Additionally, a control group (n=30) composed of subjects without any type of contact with agricultural activity was considered. All participants signed a consent form and were provided with the study protocol. Eighteen poultry workers (58.6%) and six workers from the swine production facilities (54.5%) showed detectable levels of AFB1. In the control group, the AFB1 values were all below 1 ng/ml. No significant differences in AFB1 levels in serum between workers from poultry and swine farms were found. Poultry workers, however, showed the highest serum levels and a significant statistical difference between this group and the control group was found. Results suggest that exposure to AFB1 by inhalation occurs in both occupational settings representing an additional risk that needs to be recognised, assessed and prevented.

A new frontier in biodiversity inventory: a proposal for estimators of phylogenetic and functional diversity

Copyright © 2014 The Authors. Methods in Ecology and Evolution © 2014 British Ecological Society.

Extraction of ochratoxin A in bread samples by the QuEChERS methodology

A QuEChERS method for the extraction of ochratoxin A (OTA) from bread samples was evaluated. A factorial design (23) was used to find the optimal QuEChERS parameters (extraction time, extraction solvent volume and sample mass). Extracts were analysed by LC with fluorescence detection. The optimal extraction conditions were: 5 g of sample, 15 mL of acetonitrile and 3 min of agitation. The extraction procedure was validated by systematic recovery experiments at three levels. The recoveries obtained ranged from 94.8% (at 1.0 μg kg -1) to 96.6% (at 3.0 μg kg -1). The limit of quantification of the method was 0.05 μg kg -1. The optimised procedure was applied to 20 samples of different bread types (‘‘Carcaça’’, ‘‘Broa de Milho’’, and ‘‘Broa de Avintes’’) highly consumed in Portugal. None of the samples exceeded the established European legal limit of 3 μg kg -1.

Integration of biomonitoring and instrumental techniques to assess the air quality in an industrial area located in the coastal of Central Asturias, Spain

Throughout the world, epidemiological studies were established to examine the relationship between air pollution and mortality rates and adverse respiratory health effects. However, despite the years of discussion the correlation between adverse health effects and atmospheric pollution remains controversial, partly because these studies are frequently restricted to small and well-monitored areas. Monitoring air pollution is complex due to the large spatial and temporal variations of pollution phenomena, the high costs of recording instruments, and the low sampling density of a purely instrumental approach. Therefore, together with the traditional instrumental monitoring, bioindication techniques allow for the mapping of pollution effects over wide areas with a high sampling density. In this study, instrumental and biomonitoring techniques were integrated to support an epidemiological study that will be developed in an industrial area located in Gijon in the coastal of central Asturias, Spain. Three main objectives were proposed to (i) analyze temporal patterns of PM10 concentrations in order to apportion emissions sources, (ii) investigate spatial patterns of lichen conductivity to identify the impact of the studied industrial area in air quality, and (iii) establish relationships amongst lichen conductivity with some site-specific characteristics. Samples of the epiphytic lichen Parmelia sulcata were transplanted in a grid of 18 by 20 km with an industrial area in the center. Lichens were exposed for a 5-mo period starting in April 2010. After exposure, lichen samples were soaked in 18-MΩ water aimed at determination of water electrical conductivity and, consequently, lichen vitality and cell damage. A marked decreasing gradient of lichens conductivity relative to distance from the emitting sources was observed. Transplants from a sampling site proximal to the industrial area reached values 10-fold higher than levels far from it. This finding showed that lichens reacted physiologically in the polluted industrial area as evidenced by increased conductivity correlated to contamination level. The integration of temporal PM10 measurements and analysis of wind direction corroborated the importance of this industrialized region for air quality measurements and identified the relevance of traffic for the urban area.

Adaptive mutations in bacteria: high rate and small effects

Evolution by natural selection is driven by the continuous generation of adaptive mutations. We measured the genomic mutation rate that generates beneficial mutations and their effects on fitness in Escherichia coli under conditions in which the effect of competition between lineages carrying different beneficial mutations is minimized. We found a rate on the order of 10–5 per genome per generation, which is 1000 times as high as previous estimates, and a mean selective advantage of 1%. Such a high rate of adaptive evolution has implications for the evolution of antibiotic resistance and pathogenicity.

Lipid extractions from marine deep-sea invertebrates : modifications to the Bligh & Dyer method to increase lipid yields

The deep-sea environment is difficult to sample, and often only small quantities of samples can be obtained when using less destructive methods than dredging. When working with marine animals that are difficult to sample and with limited quantities of tissue to extract lipids, it is essential to ensure that the used method extracts the maximum possible quantity of lipids. This study evaluates the efficiency of introducing modifications to the method originally described by Bligh & Dyer (1959). This lipid extraction method is broadly used with modifications, although these usually lack proper description and evaluation of increment in lipids. In this study we consider the improvement in terms of amount of lipids extracted by changing the method. Lipid content was determined by gravimetric measurements in eight invertebrates from the deep-sea, including deep-sea hydrothermal vents animals, using three different approaches. Results show increases of 14% to 30% in lipid contents obtained from hydrothermal vent invertebrate tissues and whole animals by placing the samples in methanol for 24 hours before applying the Bligh & Dyer mixture. Efficiency of the extractions using frozen and freeze-dried samples was also compared. For large sponges, the use of lyophilized materials resulted in increases of 3 to 7 times more lipids extracted when compared with extractions using frozen samples.

Avaliação do desempenho de adsorventes obtidos a partir de resíduos da indústria de curtumes na adsorção de poluentes

Na procura por uma solução de valorização dos resíduos gerados pela indústria de curtumes, o presente trabalho tem como principais objectivos a preparação de adsorventes a partir de resíduos desta actividade e a avaliação do seu desempenho na adsorção de poluentes. Para atingir este objectivo, inicialmente procedeu-se à carbonização das aparas de couro wet-white à temperatura de 800 ºC. Seguidamente, os carbonizados foram activados por activação química, tendo sido o hidróxido de potássio o agente activante escolhido. As razões mássicas hidróxido de potássio:precursor usadas na impregnação, foram iguais a 0,5:1 e 1:1. Para a razão 0,5:1, as temperaturas de activação escolhidas foram 700 e 800 ºC. Para a razão de impregnação 1:1, as temperaturas de activação usadas foram 700, 800 e 900 ºC. Para uma avaliação preliminar da capacidade de adsorção dos carvões activados produzidos, efectuou-se a determinação do número de azul de metileno. Este teste provou serem as amostras activadas a 900 ºC as que apresentaram melhores resultados (número de azul de metileno: 24g/100g) e as amostras activadas a 700 ºC, as que apresentaram menor capacidade de adsorção (1g/100g, para a razão de 0,5:1 e 7g/100g, para a razão de 1:1). Verificou-se também que amostras preparadas com iguais condições de activação (temperatura de activação e razão de impregnação), mas produzidas a partir de carbonizado de diferentes granulometrias, apresentaram diferentes desempenhos na adsorção de azul de metileno. As propriedades texturais dos carvões activados produzidos foram obtidas pela determinação das isotérmicas de adsorção de azoto a 77 K. Para tal, selecionaram-se quatro amostras: dois carvões activados a 800 ºC, com uma razão de impregnação de 1:1 e dois carvões activados a 900 ºC, com a mesma razão de impregnação, obtidos a partir de carbonizados com diferentes granulometrias. As isotérmicas obtidas são características de materiais essencialmente microporosos, com mesoporos e macroporos. Verificou-se também que a granulometria do precursor carbonizado influencia as propriedades texturais dos carvões activados produzidos. Para as temperaturas de activação usadas, 800 e 900 ºC, os carvões activados preparados a partir de carbonizado de menor granulometria apresentam melhores propriedades texturais. O carvão activado que apresentou maior área superficial específica foi obtido a 900 ºC, a partir de carbonizado finamente moído (SBET = 1475 m2/g). Determinadas as propriedades texturais dos carvões activados produzidos, realizaram-se ensaios de adsorção do corante CORIACIDE DARK BROWN VR, usado na indústria de curtumes com um carvão activado produzido no âmbito deste trabalho e com um carvão activado comercial NORIT ROW 0,8. A amostra de carvão activado produzida a partir de resíduos de wet-white escolhida para estes ensaios foi o carvão activado a 800 ºC, à razão de 1:1, a partir de carbonizado finamente moído (ww_800_1:1_carb.moído). Verificou-se que as quantidades adsorvidas pela amostra ww_800_1:1_carb.moído variaram entre os valores 7,47 e 32,07 mgcorante/gcarvão activado. Quanto ao carvão activado comercial, as quantidades adsorvidas situaram-se entre 8,95 e 69,13 mgcorante/gcarvão activado. Assim, conclui-se que o carvão activado comercial apresentou melhor desempenho na adsorção do corante da indústria de curtumes. Os carvões activados obtidos revelaram-se materiais essencialmente microporosos, com capacidade de adsorção de poluentes, como por exemplo corantes, no entanto o seu desempenho seria mais eficaz na adsorção de pequenas moléculas devido ao elevado volume de microporos que apresentaram.

Optimal strategies for marine wildlife tourism in small islands

Tese de Doutoramento, Ciências Económicas e Empresariais (especialidade de Economia), 18 de Junho de 2015, Universidade dos Açores

Determinação de propriedades mecânicas através de ensaios de provetes miniatura, "Small Punch"

Trabalho Final de Mestrado para obtenção do grau de Mestre em Engenharia Mecânica

Survey of trace elements (Al, As, Cd, Cr, Co, Hg, Mn, Ni, Pb, Se, and Si) in retail samples of flavoured and bottled waters

Concentrations of eleven trace elements (Al, As, Cd, Cr, Co, Hg, Mn, Ni, Pb, Se, and Si) were measured in 39 (natural and flavoured) water samples. Determinations were performed using graphite furnace electrothermetry for almost all elements (Al, As, Cd, Cr, Co, Mn, Ni, Pb, and Si). For Se determination hydride generation was used, and cold vapour generation for Hg. These techniques were coupled to atomic absorption spectrophotometry. The trace element content of still or sparkling natural waters changed from brand to brand. Significant differences between natural still and natural sparkling waters (p<0.001) were only apparent for Mn. The Mann–Whitney U-test was used to search for significant differences between flavoured and natural waters. The concentration of each element was compared with the presence of flavours, preservatives, acidifying agents, fruit juice and/or sweeteners, according to the labelled composition. It was shown that flavoured waters generally increase the trace element content. The addition of preservatives and acidifying regulators had a significant influence on Mn, Co, As and Si contents (p<0.05). Fruit juice can also be correlated to the increase of Co and As. Sweeteners did not provide any significant difference in Mn, Co, Se and Si content.

New biomimetic sensors for the determination of tetracycline in biological samples: batch and flow mode operations

New potentiometric membrane sensors with cylindrical configuration for tetracycline (TC) are described based on the use of a newly designed molecularly imprinted polymer (MIP) material consisting of 2-vinylpyridine as a functional monomer in a plasticized PVC membrane. The sensor exhibited significantly enhanced response towards TC over the concentration range 1.59 10 5–1.0 10 3 mol L 1 at pH 3–5 with a lower detection limit of 1.29 10 5 mol L 1. The response was near-Nernstian, with average slopes of 63.9 mV decade 1. The effect of lipophilic salts and various foreign common ions were tested and were found to be negligible. The possibility of applying the proposed sensor to TC determination in spiked biological fluid samples was demonstrated.

Analysis of polycyclic aromatic hydrocarbons in atmospheric particulate samples by microwaveassisted extraction and liquid chromatography

A methodology based on microwave-assisted extraction (MAE) and LC with fluorescence detection (FLD) was investigated for the efficient determination of 15 polycyclic aromatic hydrocarbons (PAHs) regarded as priority pollutants by the US Environmental Protection Agency and dibenzo(a,l)pyrene in atmospheric particulate samples. PAHs were successfully extracted from real outdoor particulate matter (PM) samples with recoveries ranging from 81.4±8.8 to 112.0±1.1%, for all the compounds except for naphthalene (62.3±18.0%) and anthracene (67.3±5.7%), under the optimum MAE conditions (30.0 mL of ACN for 20 min at 110ºC). No clean-up steps were necessary prior to LC analysis. LOQs ranging from 0.0054 ng/m3 for benzo( a)anthracene to 0.089 ng/m3 for naphthalene were reached. The validated MAE methodology was applied to the determination of PAHs from a set of real world PM samples collected in Oporto (north of Portugal). The sum of particulate-bound PAHs in outdoor PM ranged from 2.5 and 28 ng/m3.

Screening of carbamates and ureas in fresh and processed tomato samples using micowave-assisted extraction and liquid chromatography

An analytical method, based on microwave-assisted extraction and liquid chromatography with diode array detection, for the determination of six carbamate and three urea pesticides in fresh and processed tomato samples is described. Significant parameters affecting extraction efficiency were optimized. Under optimum microwave-assisted extraction conditions (20mL acetonitrile, for 10 minutes, at 60º C), pesticides were extracted with recoveries ranging from 57.6 to 102% (RSDs<7%). Quantification limits between 6.5 and 39.6 µg=kg were obtained. A total number of 28 different fresh tomato samples and 6 processed tomato products were analysed. Confirmation of suspicious samples was performed by LC-MS.