Integrative Pathway Analysis Using Graph-Based Learning with Applications to TCGA Colon and Ovarian Data

published_or_final_versio

Commercial yeast utilization and genetic structure of vineyard-associated Saccharomyces cerevisiae populations revealed by microsatellite analysis

Since the beginning of the 1980’s, the use of active dried Saccharomyces cerevisiae yeast starters has been extensively generalised. Today, the majority of wine production is based on the use of active dried yeast, which ensures rapid and reliable fermentations. The behaviour of these yeasts in the ecosystem of the vineyard is totally unknown as is their potential impact on the natural microflora. The aim of the present study was to evaluate populational structures among fermenting S. cerevisiae populations and to assess the impact of active dry yeast usage on the genetic structures of the vineyard microflora. Saccharomyces cerevisiae isolates were obtained from fermentations with grapes from three vineyards of the Vinho Verde Region where commercial yeast strains were used continuously during the last years. Populational genetic analysis was based on six polymorphic microsatellite loci in 361 isolates. Accumulation of small allele-frequency differences across six loci in groups of strains allowed the identification of populational structures. The continuous use of active dry yeast has a very limited impact on the genetic structure of the vineyard microflora. Correlation of genetic differentiation with the distance between sampling points suggested a pattern of isolation-by-distance, where genetic divergence in a vineyard increased with size.Financially supported by the programs POCI 2010 (FEDER/FCT, POCTI/AGR/56102/2004) and AGRO (ENOSAFE, Nº 762)

Identification of wine related yeast species by capillary electrophoresis single strand conformation polymorphism analysis (CE-SSCP) of the 26S rRNA Gene

Financially supported by the programs POCI 2010 (FEDER/FCT, POCTI/AGR/56102/2004, POCTI/AGR/56771/2004), and AGRO (ENOSAFE, Nº 762)

Identification of wine related yeast species by capillary electrophoresis single- strand conformation polymorphism

Fundação para a Ciência e a Tecnologia (FCT) - POCI 2010; POCTI/AGR/56102/2004.FEDER.AGRO (ENOSAFE, Nº 762)

Origin and Health Impacts of Emissions of Toxic By-Products and Fine Particles from Combustion and Thermal Treatment of Hazardous Wastes and Materials

High-temperature, controlled incineration and thermal treatment of contaminated soils, sediments, and wastes at Superfund sites are often preferred methods of remediation of contaminated sites under the Comprehensive Environmental Response, Compensation, and Liability Act of 1980 and related legislation. Although these methods may be executed safely, formation of toxic combustion or reaction by-products is still a cause of concern. Emissions of polycyclic aromatic hydrocarbons (PAHs); chlorinated hydrocarbons (CHCs), including polychlorinated dibenzo-p-dioxins and dibenzofurans; and toxic metals (e.g., chromium VI) have historically been the focus of combustion and health effects research. However, fine particulate matter (PM) and ultrafine PM, which have been documented to be related to cardiovascular disease, pulmonary disease, and cancer, have more recently become the focus of research. Fine PM and ultrafine PM are effective delivery agents for PAHs, CHCs, and toxic metals. In addition, it has recently been realized that brominated hydrocarbons (including brominated/chlorinated dioxins), redox-active metals, and redox-active persistent free radicals are also associated with PM emissions from combustion and thermal processes. In this article, we discuss the origin of each of these classes of pollutants, the nature of their association with combustion-generated PM, and the mechanisms of their known and potential health impacts

Compensatory growth in oceanic loggerhead sea turtles: response to a stochastic environment

Compensatory growth (CG, accelerated growth that may occur when an organism that has grown at a reduced rate as a result of suboptimal environmental conditions is exposed to better conditions) is considered an adaptation to variable en vironments. Although documented thoroughly under captive conditions, CG has rarely been studied in wild populations. In their first years of life, oceanic-stage loggerhead sea turtles (Caretta caretta) have relatively little control over their geographic position or movements and thus have an extremely stochastic lifestyle with great variation in food availability and temperature. This environmental variation results in variable growth rates. We evaluate somatic growth functions of oceanic-stage loggerheads from the eastern Atlantic based on skeletochronology that allowed us to assign age and cohort to each individual. We demonstrate CG in these turtles based on three different analytical approaches: changes in coefficients of variation in size-at-age, generalized additive model regression analyses of somatic growth, and linear regression of age-specific growth rates. As a result of CG, variation in size-at-age in these juvenile loggerheads is substantially reduced. Thus, size is a better predictor of age than expected based on variation in growth rates. CG decreases with age, apparently as loggerheads gain greater control over their movements. In addition, we have evaluated for the first time in wild sea turtles the time-dependent nature of somatic growth by distinguishing among age, year, and cohort effects using a mixed longitudinal sampling design with assigned-age individuals. Age and year had significant effects on growth rates, but there was no significant cohort effect. Our results address critical gaps in knowledge of the demog raphy of this endangered species.info:eu-repo/semantics/publishedVersio

Environmentally persistent free radicals amplify ultrafine particle mediated cellular oxidative stress and cytotoxicity

<p>Abstract</p> <p>Background</p> <p>Combustion generated particulate matter is deposited in the respiratory tract and pose a hazard to the lungs through their potential to cause oxidative stress and inflammation. We have previously shown that combustion of fuels and chlorinated hydrocarbons produce semiquinone-type radicals that are stabilized on particle surfaces (i.e. environmentally persistent free radicals; EPFRs). Because the composition and properties of actual combustion-generated particles are complex, heterogeneous in origin, and vary from day-to-day, we have chosen to use surrogate particle systems. In particular, we have chosen to use the radical of 2-monochlorophenol (MCP230) as the EPFR because we have previously shown that it forms a EPFR on Cu(II)O surfaces and catalyzes formation of PCDD/F. To understand the physicochemical properties responsible for the adverse pulmonary effects of combustion by-products, we have exposed human bronchial epithelial cells (BEAS-2B) to MCP230 or the CuO/silica substrate. Our general hypothesis was that the EPFR-containing particle would have greater toxicity than the substrate species.</p> <p>Results</p> <p>Exposure of BEAS-2B cells to our combustion generated particle systems significantly increased reactive oxygen species (ROS) generation and decreased cellular antioxidants resulting in cell death. Resveratrol treatment reversed the decline in cellular glutathione (GSH), glutathione peroxidase (GPx), and superoxide dismutase (SOD) levels for both types of combustion-generated particle systems.</p> <p>Conclusion</p> <p>The enhanced cytotoxicity upon exposure to MCP230 correlated with its ability to generate more cellular oxidative stress and concurrently reduce the antioxidant defenses of the epithelial cells (i.e. reduced GSH, SOD activity, and GPx). The EPFRs in MCP230 also seem to be of greater biological concern due to their ability to induce lipid peroxidation. These results are consistent with the oxidizing nature of the CuO/silica ultrafine particles and the reducing nature and prolonged environmental and biological lifetimes of the EPFRs in MCP230.</p

The implausibility of ‘usual care’ in an open system: sedation and weaning practices in Paediatric Intensive Care Units (PICUs) in the United Kingdom (UK)

Background: The power of the randomised controlled trial depends upon its capacity to operate in a closed system whereby the intervention is the only causal force acting upon the experimental group and absent in the control group, permitting a valid assessment of intervention efficacy. Conversely, clinical arenas are open systems where factors relating to context, resources, interpretation and actions of individuals will affect implementation and effectiveness of interventions. Consequently, the comparator (usual care) can be difficult to define and variable in multi-centre trials. Hence outcomes cannot be understood without considering usual care and factors that may affect implementation and impact on the intervention. Methods: Using a fieldwork approach, we describe PICU context, ‘usual’ practice in sedation and weaning from mechanical ventilation, and factors affecting implementation prior to designing a trial involving a sedation and ventilation weaning intervention. We collected data from 23 UK PICUs between June and November 2014 using observation, individual and multi-disciplinary group interviews with staff. Results: Pain and sedation practices were broadly similar in terms of drug usage and assessment tools. Sedation protocols linking assessment to appropriate titration of sedatives and sedation holds were rarely used (9 % and 4 % of PICUs respectively). Ventilator weaning was primarily a medical-led process with 39 % of PICUs engaging senior nurses in the process: weaning protocols were rarely used (9 % of PICUs). Weaning methods were variably based on clinician preference. No formal criteria or use of spontaneous breathing trials were used to test weaning readiness. Seventeen PICUs (74 %) had prior engagement in multi-centre trials, but limited research nurse availability. Barriers to previous trial implementation were intervention complexity, lack of belief in the evidence and inadequate training. Facilitating factors were senior staff buy-in and dedicated research nurse provision. Conclusions: We examined and identified contextual and organisational factors that may impact on the implementation of our intervention. We found usual practice relating to sedation, analgesia and ventilator weaning broadly similar, yet distinctively different from our proposed intervention, providing assurance in our ability to evaluate intervention effects. The data will enable us to develop an implementation plan; considering these factors we can more fully understand their impact on study outcomes