Antimicrobial use and incidence of multidrug-resistant Pseudomonas aeruginosa in a teaching hospital: an ecological approach

INTRODUCTION: Multidrug-resistant Pseudomonas aeruginosa is a major threat in healthcare settings. The use of antimicrobials can influence the incidence of resistant strains by direct and indirect mechanisms. The latter can be addressed by ecological studies. METHODS: Our group attempted to analyze the relation between the use of antipseudomonal drugs and the incidence of MDR-PA among 18 units from a 400-bed teaching hospital. The study had a retrospective, ecological design, comprising data from 2004 and 2005. Data on the use of four antimicrobials (amikacin, ciprofloxacin, ceftazidime and imipenem) were tested for correlation with the incidence of MDR-PA (defined as isolates resistant to the four antimicrobials of interest) in clinical cultures. Univariate and multivariate linear regression analyses were performed. RESULTS: Significant correlations were determined between use and resistance for all antimicrobials in the univariate analysis: amikacin (standardized correlation coefficient = 0.73, p = 0.001); ciprofloxacin (0.71, p = 0.001); ceftazidime (0.61, p = 0.007) and imipenem (0.87, p < 0.001). In multivariate analysis, only imipenem (0.67, p = 0.01) was independently related to the incidence of multidrug-resistant strains. CONCLUSIONS: These findings share similarities with those reported in individual-based observational studies, with possible implications for infection control.

Analysis of temporal and spatial variations of forest. A case of study in notheastern Armenia

The forest has a crucial ecological role and the continuous forest loss can cause colossal effects on the environment. As Armenia is one of the low forest covered countries in the world, this problem is more critical. Continuous forest disturbances mainly caused by illegal logging started from the early 1990s had a huge damage on the forest ecosystem by decreasing the forest productivity and making more areas vulnerable to erosion. Another aspect of the Armenian forest is the lack of continuous monitoring and absence of accurate estimation of the level of cuts in some years. In order to have insight about the forest and the disturbances in the long period of time we used Landsat TM/ETM + images. Google Earth Engine JavaScript API was used, which is an online tool enabling the access and analysis of a great amount of satellite imagery. To overcome the data availability problem caused by the gap in the Landsat series in 1988- 1998, extensive cloud cover in the study area and the missing scan lines, we used pixel based compositing for the temporal window of leaf on vegetation (June-late September). Subsequently, pixel based linear regression analyses were performed. Vegetation indices derived from the 10 biannual composites for the years 1984-2014 were used for trend analysis. In order to derive the disturbances only in forests, forest cover layer was aggregated and the original composites were masked. It has been found, that around 23% of forests were disturbed during the study period.

Analysis and visualization of energy use for university campus

The reduction of greenhouse gas emissions is one of the big global challenges for the next decades due to its severe impact on the atmosphere that leads to a change in the climate and other environmental factors. One of the main sources of greenhouse gas is energy consumption, therefore a number of initiatives and calls for awareness and sustainability in energy use are issued among different types of institutional and organizations. The European Council adopted in 2007 energy and climate change objectives for 20% improvement until 2020. All European countries are required to use energy with more efficiency. Several steps could be conducted for energy reduction: understanding the buildings behavior through time, revealing the factors that influence the consumption, applying the right measurement for reduction and sustainability, visualizing the hidden connection between our daily habits impacts on the natural world and promoting to more sustainable life. Researchers have suggested that feedback visualization can effectively encourage conservation with energy reduction rate of 18%. Furthermore, researchers have contributed to the identification process of a set of factors which are very likely to influence consumption. Such as occupancy level, occupants behavior, environmental conditions, building thermal envelope, climate zones, etc. Nowadays, the amount of energy consumption at the university campuses are huge and it needs great effort to meet the reduction requested by European Council as well as the cost reduction. Thus, the present study was performed on the university buildings as a use case to: a. Investigate the most dynamic influence factors on energy consumption in campus; b. Implement prediction model for electricity consumption using different techniques, such as the traditional regression way and the alternative machine learning techniques; and c. Assist energy management by providing a real time energy feedback and visualization in campus for more awareness and better decision making. This methodology is implemented to the use case of University Jaume I (UJI), located in Castellon, Spain.

Spatio-temporal patterns of tuberculosis incidence in Ribeirão Preto, State of São Paulo, southeast Brazil, and their relationship with social vulnerability: a Bayesian analysis

INTRODUCTION: The purpose of this ecological study was to evaluate the urban spatial and temporal distribution of tuberculosis (TB) in Ribeirão Preto, State of São Paulo, southeast Brazil, between 2006 and 2009 and to evaluate its relationship with factors of social vulnerability such as income and education level. METHODS: We evaluated data from TBWeb, an electronic notification system for TB cases. Measures of social vulnerability were obtained from the SEADE Foundation, and information about the number of inhabitants, education and income of the households were obtained from Brazilian Institute of Geography and Statistics. Statistical analyses were conducted by a Bayesian regression model assuming a Poisson distribution for the observed new cases of TB in each area. A conditional autoregressive structure was used for the spatial covariance structure. RESULTS: The Bayesian model confirmed the spatial heterogeneity of TB distribution in Ribeirão Preto, identifying areas with elevated risk and the effects of social vulnerability on the disease. We demonstrated that the rate of TB was correlated with the measures of income, education and social vulnerability. However, we observed areas with low vulnerability and high education and income, but with high estimated TB rates. CONCLUSIONS: The study identified areas with different risks for TB, given that the public health system deals with the characteristics of each region individually and prioritizes those that present a higher propensity to risk of TB. Complex relationships may exist between TB incidence and a wide range of environmental and intrinsic factors, which need to be studied in future research.

Analysis of metabolic flux distributions in relation to the extracellular environment in Avian cells

Continuous cell lines that proliferate in chemically defined and simple media have been highly regarded as suitable alternatives for vaccine production. One such cell line is the AG1.CR.pIX avian cell line developed by PROBIOGEN. This cell line can be cultivated in a fully scalable suspension culture and adapted to grow in chemically defined, calf serum free, medium [1]–[5]. The medium composition and cultivation strategy are important factors for reaching high virus titers. In this project, a series of computational methods was used to simulate the cell’s response to different environments. The study is based on the metabolic model of the central metabolism proposed in [1]. In a first step, Metabolic Flux Analysis (MFA) was used along with measured uptake and secretion fluxes to estimate intracellular flux values. The network and data were found to be consistent. In a second step, Flux Balance Analysis (FBA) was performed to access the cell’s biological objective. The objective that resulted in the best predicted results fit to the experimental data was the minimization of oxidative phosphorylation. Employing this objective, in the next step Flux Variability Analysis (FVA) was used to characterize the flux solution space. Furthermore, various scenarios, where a reaction deletion (elimination of the compound from the media) was simulated, were performed and the flux solution space for each scenario was calculated. Growth restrictions caused by essential and non-essential amino acids were accurately predicted. Fluxes related to the essential amino acids uptake and catabolism, the lipid synthesis and ATP production via TCA were found to be essential to exponential growth. Finally, the data gathered during the previous steps were analyzed using principal component analysis (PCA), in order to assess potential changes in the physiological state of the cell. Three metabolic states were found, which correspond to zero, partial and maximum biomass growth rate. Elimination of non-essential amino acids or pyruvate from the media showed no impact on the cell’s assumed normal metabolic state.

Should Quinta dos Açores expand its retailer network in lisbon?

The primary purpose of this research is to examine the feasibility of expanding Quinta dos Açores retailer network in Lisbon starting from 2015 onwards. A time series model was developed to estimate the company’s future production and sales. A Discounted Cash Flow analysis was also conducted to determine the profitability of this expansion opportunity. Our findings reveal that Quinta dos Açores will face negative results in the first two years of the expansion strategy, but the overall opportunity presents a net positive result of almost three million euros.

Ecological competition and the incidence of Acinetobacter baumannii bloodstream infections in a teaching hospital in Southeastern Brazil

IntroductionRecently, pathogen ecology has been recognized as an important epidemiological determinant of healthcare-associated infections (HAIs). Acinetobacter baumannii is one of the most important agents known to cause HAIs. It is widespread in healthcare settings and exhibits seasonal variations in incidence. Little is known about the impact of competition with other hospital pathogens on the incidence of A. baumannii infection.MethodsWe conducted an ecological study, enrolling patients who presented with healthcare-associated bloodstream infections (HA-BSIs) from 2005 to 2010 at a 450-bed teaching hospital in Brazil. HA-BSIs were said to be present when bacteria or fungi were recovered from blood cultures collected at least three days after admission. Monthly incidence rates were calculated for all HA-BSIs (overall or caused by specific pathogens or groups of pathogens). Multivariate Poisson regression models were used to identify the impacts of the incidence of several pathogens on the incidence of A. baumannii.ResultsThe overall incidence rate of HA-BSI caused by A. baumannii was 2.5 per 10,000 patient-days. In the multivariate analysis, the incidence of HA-BSI caused by A. baumanniiwas negatively associated with the incidence rates of HA-BSI due to Staphylococcus aureus (rate ratio [RR]=0.88; 95% confidence interval [CI]=0.80-0.97), Enterobacter spp. (RR=0.84; 95%CI=0.74-0.94) and a pool of less common gram-negative pathogens.ConclusionsOur results suggest that competition between pathogens influences the etiology of HA-BSIs. It would be beneficial to take these findings into account in infection control policies.

Occurrence of severe dengue in Rio de Janeiro: an ecological study

Introduction This study aimed to analyze the relationship between the incidence of severe dengue during the 2008 epidemic in Rio de Janeiro, Brazil, and socioeconomic indicators, as well as indicators of health service availability and previous circulation of the dengue virus serotype-3 (DENV-3). Methods In this ecological study, the units of analysis were the districts of Rio de Janeiro. The data were incorporated into generalized linear models, and the incidence of severe dengue in each district was the outcome variable. Results The districts with more cases of dengue fever in the 2001 epidemic and a higher percentage of residents who declared their skin color or race as black had higher incidence rates of severe dengue in the 2008 epidemic [incidence rate ratio (IRR)= 1.21; 95% confidence interval (95%CI)= 1.05-1.40 and IRR= 1.34; 95%CI= 1.16-1.54, respectively]. In contrast, the districts with Family Health Strategy (FHS) clinics were more likely to have lower incidence rates of severe dengue in the 2008 epidemic (IRR= 0.81; 95%CI= 0.70-0.93). Conclusions At the ecological level, our findings suggest the persistence of health inequalities in this region of Brazil that are possibly due to greater social vulnerability among the self-declared black population. Additionally, the protective effect of FHS clinics may be due to the ease of access to other levels of care in the health system or to a reduced vulnerability to dengue transmission that is afforded by local practices to promote health.

Exploring Literary Landscapes: From Texts to Spatiotemporal Analysis through Collaborative Work and GIS

This article argues that the study of literary representations of landscapes can be aided and enriched by the application of digital geographic technologies. As an example, the article focuses on the methods and preliminary findings of LITESCAPE.PT—Atlas of Literary Landscapes of Mainland Portugal, an on-going project that aims to study literary representations of mainland Portugal and to explore their connections with social and environmental realities both in the past and in the present. LITESCAPE.PT integrates traditional reading practices and ‘distant reading’ approaches, along with collaborative work, relational databases, and geographic information systems (GIS) in order to classify and analyse excerpts from 350 works of Portuguese literature according to a set of ecological, socioeconomic, temporal and cultural themes. As we argue herein this combination of qualitative and quantitative methods—itself a response to the difficulty of obtaining external funding—can lead to (a) increased productivity, (b) the pursuit of new research goals, and (c) the creation of new knowledge about natural and cultural history. As proof of concept, the article presents two initial outcomes of the LITESCAPE.PT project: a case study documenting the evolving literary geography of Lisbon and a case study exploring the representation of wolves in Portuguese literature.

Critical analysis of the allocation policy for liver transplantation in Brazil

Liver transplantation is now the standard treatment for end-stage liver disease. Given the shortage of liver donors and the progressively higher number of patients waiting for transplantation, improvements in patient selection and optimization of timing for transplantation are needed. Several solutions have been suggested, including increasing the donor pool; a fair policy for allocation, not permitting variables such as age, gender, and race, or third-party payer status to play any role; and knowledge of the natural history of each liver disease for which transplantation is offered. To observe ethical rules and distributive justice (guarantee to every citizen the same opportunity to get an organ), the "sickest first" policy must be used. Studies have demonstrated that death has no relationship with waiting time, but rather with the severity of liver disease at the time of inclusion. Thus, waiting time is no longer part of the United Network for Organ Sharing distribution criteria. Waiting time only differentiates between equally severely diseased patients. The authors have analyzed the waiting list mortality and 1-year survival for patients of the State of São Paulo, from July 1997 through January 2001. Only the chronological criterion was used. According to "Secretaria de Estado da Saúde de São Paulo" data, among all waiting list deaths, 82.2% occurred within the first year, and 37.6% within the first 3 months following inclusion. The allocation of livers based on waiting time is neither fair nor ethical, impairs distributive justice and human rights, and does not occur in any other part of the world.

Risk acceptance in the furniture sector: Analysis of acceptance level and relevant influence factors

Risk acceptance has been broadly discussed in relation to hazardous risk activities and/or technologies. A better understanding of risk acceptance in occupational settings is also important; however, studies on this topic are scarce. It seems important to understand the level of risk that stakeholders consider sufficiently low, how stakeholders form their opinion about risk, and why they adopt a certain attitude toward risk. Accordingly, the aim of this study is to examine risk acceptance in regard to occupational accidents in furniture industries. The safety climate analysis was conducted through the application of the Safety Climate in Wood Industries questionnaire. Judgments about risk acceptance, trust, risk perception, benefit perception, emotions, and moral values were measured. Several models were tested to explain occupational risk acceptance. The results showed that the level of risk acceptance decreased as the risk level increased. High-risk and death scenarios were assessed as unacceptable. Risk perception, emotions, and trust had an important influence on risk acceptance. Safety climate was correlated with risk acceptance and other variables that influence risk acceptance. These results are important for the risk assessment process in terms of defining risk acceptance criteria and strategies to reduce risks.

Modeling microbes: New methods for integrated metabolic and regulatory network reconstruction

PhD Thesis in Bioengineering

A new empirical system for rock slope stability analysis in exploitation stage

An empirical system was developed to obtain a quality index for rock slopes in road infrastructures, named Slope Quality Index (SQI), and it was applied to a set of real slopes.The SQI is supported in nine factors affecting slope stability that contemplate the evaluation of different parameters. Consequently, each factor is classified by the degree of importance and influence by assigned weights. These weights were established through a statistical analysis of replies to a survey that was distributed to several experienced professionals in the field. The proposed SQI varies between1 and 5, corresponding to slopes in very good and very bad condition state, respectively. Besides the advantage linked to a quantitative and qualitative evaluation of slopes, theSQI also allows identifying the most critical factors on the slope stability, which is a fundamental issue for an efficient management of the slope network in the road infrastructure, namely in the planning of conservation and maintenance operations.

Genetic diversity in rosewood saplings (Aniba rosaeodora ducke, Lauraceae): an ecological approach

This article takes an ecological approach to the genetic diversity of Rosewood (Aniba rosaeodora Ducke) in a central Amazonian terra firme forest north of Manaus. Planted Rosewood setting, under partial shaded canopy, were assessed in terms of fruiting production, frugivory, and seed dispersal. Using RAPD molecular analysis procedures, the influence of the spatial distribution of adult trees on the genetic diversity (polymorphism) of saplings was assessed with genetic samples from 34 reproductive trees and 60 saplings. The density and distribution patterns the reproductive trees did not modify the sapling"s diversity (1.86%, AMOVA). Two types of adult tree dispersion were identified; i) clumped and ii) more widely dispersed. Polymorphism (77.5%) and gene flow were high between these. Although more sapling genetic variability in areas with a higher density of mature plants was not as high as expected, density did not affect the genetic diversity of samplings, indicating a high incidence of gene flow amongst trees. In planted Rosewood population (surrounded by low disturbed forest), fruiting trees experienced a high level of removal of seeds by toucans (Rhamphastidae), about of 50%. The high gene flow found among native trees suggested that toucans, promoting seed rain at short and long distances from maternal trees, actively contribute to the maintenance of genetic diversity within wild rosewood populations.

Differential activation of the default mode network in jet lagged individuals

Long-term exposure to transmeridian flights has been shown to impact cognitive functioning. Nevertheless, the immediate effects of jet lag in the activation of specific brain networks have not been investigated. We analyzed the impact of short-term jet lag on the activation of the default mode network (DMN). A group of individuals who were on a transmeridian flight and a control group went through a functional magnetic resonance imaging acquisition. Statistical analysis was performed to test for differences in the DMN activation between groups. Participants from the jet lag group presented decreased activation in the anterior nodes of the DMN, specifically in bilateral medial prefrontal and anterior cingulate cortex. No areas of increased activation were observed for the jet lag group. These results may be suggestive of a negative impact of jet lag on important cognitive functions such as introspection, emotional regulation and decision making in a few days after individuals arrive at their destination.