Contribution to economic evaluation of systems that value animal welfare at farm

The demand for "welfare friendly" products increases as public conscience and perception on livestock production systems grow. The public and policy-makers demand scientific information for education and to guide decision processes. This paper describes some of the last decade contributions made by scientists on the technical, economical and market areas of farm animal welfare. Articles on animal welfare were compiled on the following themes: 1) consumer behavior, 2) technical and economical viability, 3) public regulation, and 4) private certification policies. Most studies on the economic evaluation of systems that promote animal welfare involved species destined to produce export items, such as eggs, beef and pork. Few studies were found on broilers, dairy cows and fish, and data regarding other species, such as horses, sheep and goats were not found. Scientists understand that farm animal welfare is not only a matter of ethics, but also an essential tool to gain and maintain markets. However, it is unfortunate that little attention is paid to species that are not economically important for exports. Studies that emphasize on more humane ways to raise animals and that provide economic incentives to the producer are needed. An integrated multidisciplinary approach is necessary to highlight the benefits of introducing animal welfare techniques to existing production systems.

An integrated approach of software development and test processes to distributed teams

The Distributed Software Development (DSD) is a development strategy that meets the globalization needs concerned with the increase productivity and cost reduction. However, the temporal distance, geographical dispersion and the socio-cultural differences, increased some challenges and, especially, added new requirements related with the communication, coordination and control of projects. Among these new demands there is the necessity of a software process that provides adequate support to the distributed software development. This paper presents an integrated approach of software development and test that considers distributed teams peculiarities. The approach purpose is to offer support to DSD, providing a better project visibility, improving the communication between the development and test teams, minimizing the ambiguity and difficulty to understand the artifacts and activities. This integrated approach was conceived based on four pillars: (i) to identify the DSD peculiarities concerned with development and test processes, (ii) to define the necessary elements to compose the integrated approach of development and test to support the distributed teams, (iii) to describe and specify the workflows, artifacts, and roles of the approach, and (iv) to represent appropriately the approach to enable the effective communication and understanding of it.

An integrated approach to evaluate emerging contaminants in drinking water

The chemical stock of emerging contaminants in Brazilian drinking water is of great interest due to the poor water quality at surface water intakes. In addition, little is known about the effect of some contaminants, such as endocrine disrupting chemicals (EDCs), which may be present in both raw and treated water. The aim of this work was to evaluate selected emerging contaminants in Brazilian waters using both chemical and biological analyses. Sampling sites were established in different municipalities based upon raw water quality data. Estrone, 17 beta-estradiol, estriol, 17 alpha-ethinylestradiol, bisphenol A, 4-n-octylphenol and 4-n-nonylphenol were determined in the samples by liquid chromatography-tandem mass spectrometry. A yeast assay using a Saccharomyces cerevisiae bioluminescent bioreporter was used to evaluate the estrogenic activity of the water samples. The first integrated results revealed similarities between the two individual approaches, since higher values for the bioassay were accompanied by significant concentrations of some selected compounds in surface water samples. No estrogenicity was observed for drinking water samples. Our results also indicate that the usual paradigm of evaluating water quality by measuring selected EDCs in a given water sample via chemical analysis, needs to be reviewed since the observed estrogenicity of a water sample is now a better guiding parameter to the selection of samples and substances to be chemically investigated in further analysis. So far, the data bank produced in this work, i.e., the comparison between chemical burden and observed estrogenicity, is not yet sufficiently robust to fully guide this decision. (C) 2011 Elsevier B.V. All rights reserved.

An integrated approach to remanufacturing: model of a remanufacturing system

Remanufacturing is the process of rebuilding used products that ensures that the quality of remanufactured products is equivalent to that of new ones. Although the theme is gaining ground, it is still little explored due to lack of knowledge, the difficulty of visualizing it systemically, and implementing it effectively. Few models treat remanufacturing as a system. Most of the studies still treated remanufacturing as an isolated process, preventing it from being seen in an integrated manner. Therefore, the aim of this work is to organize the knowledge about remanufacturing, offering a vision of remanufacturing system and contributing to an integrated view about the theme. The methodology employed was a literature review, adopting the General Theory of Systems to characterize the remanufacturing system. This work consolidates and organizes the elements of this system, enabling a better understanding of remanufacturing and assisting companies in adopting the concept.

Integrated biomarker responses as environmental status descriptors of a coastal zone (Sao Paulo, Brazil)

Sao Paulo state (Brazil) has one of the most overpopulated coastal zones in South America, where previous studies have already detected sediment and water contamination. However, biological-based monitoring considering signals of xenobiotic exposure and effects are scarce. The present study employed a battery of biomarkers under field conditions to assess the environmental quality of this coastal zone. For this purpose, the activity of CYP 450, antioxidant enzymes, DNA damage, lipid peroxidation and lysosomal membrane were analysed in caged mussels and integrated using Factorial Analysis. A representation of estimated factor scores was performed in order to confirm the factor descriptions characterizing the studied areas. Biomarker responses indicated signals of mussels` impaired health during the monitoring, which pointed to the impact of different sources of contaminants in the water quality and identified critical areas. This integrated approach produced a rapid, sensitive and cost-effective assessment, which could be incorporated as a descriptor of environmental status in future coastal zones biomonitoring. (C) 2011 Elsevier Inc. All rights reserved.

Integrated sediment quality assessment in Paranagua Estuarine System, Southern Brazil

Sediment quality from Paranagua Estuarine System (PES), a highly important port and ecological zone, was evaluated by assessing three lines of evidence: (1) sediment physical-chemical characteristics; (2) sediment toxicity (elutriates, sediment-water interface, and whole sediment); and (3) benthic community structure. Results revealed a gradient of increasing degradation of sediments (i.e. higher concentrations of trace metals, higher toxicity, and impoverishment of benthic community structure) towards inner PES. Data integration by principal component analysis (PCA) showed positive correlation between some contaminants (mainly As, Cr, Ni, and Pb) and toxicity in samples collected from stations located in upper estuary and one station placed away from contamination sources. Benthic community structure seems to be affected by both pollution and natural fine characteristics of the sediments, which reinforces the importance of a weight-of-evidence approach to evaluate sediments of PES. (C) 2008 Elsevier Inc. All rights reserved.

Anthropogenic influences in a lagoonal environment: a multiproxy approach at the valo grande mouth, Cananéia-Iguape system (SE Brazil)

The Cananeia-Iguape system, SE Brazil, consists of a complex of lagoonal channels, located in a United Nations Educational, Scientific and Cultural Organization (UNESCO) Biosphere Reserve. Nevertheless, important environmental changes have occurred in approximately the last 150 yrs due to the opening of an artificial channel, the Valo Grande, connecting the Ribeira de Iguape River to the lagoonal system. Our objective is to assess the historical record of the uppermost layers of the sedimentary column of the lagoonal system in order to determine the history of environmental changes caused by the opening of the artificial channel. In this sense, an integrated geochemical-faunal approach is used. The environmental changes led significant modifications in salinity, in changes of the depositional patterns of sediments and foraminiferal assemblages (including periods of defaunation), and, more drastically, in the input of heavy metals to the coastal environment. The concentrations Pb in the core analyzed here were up to two times higher than the values measured in contaminated sediments from the Santos estuary, the most industrialized coastal zone in Brazil.

Integrated ecological risk assessment of pesticides in tropical ecosystems: A case study with carbofuran in Brazil

The aim of the present study is to contribute an ecologically relevant assessment of the ecotoxicological effects of pesticide applications in agricultural areas in the tropics, using an integrated approach with information gathered from soil and aquatic compartments. Carbofuran, an insecticide/nematicide used widely on sugarcane crops, was selected as a model substance. To evaluate the toxic effects of pesticide spraying for soil biota, as well as the potential indirect effects on aquatic biota resulting from surface runoff and/or leaching, field and laboratory (using a cost-effective simulator of pesticide applications) trials were performed. Standard ecotoxicological tests were performed with soil (Eisenia andrei, Folsomia candida, and Enchytraeus crypticus) and aquatic (Ceriodaphnia silvestrii) organisms, using serial dilutions of soil, eluate, leachate, and runoff samples. Among soil organisms, sensitivity was found to be E. crypticus < E. andrei < F. candida. Among the aqueous extracts, mortality of C. silvestrii was extreme in runoff samples, whereas eluates were by far the least toxic samples. A generally higher toxicity was found in the bioassays performed with samples from the field trial, indicating the need for improvements in the laboratory simulator. However, the tool developed proved to be valuable in evaluating the toxic effects of pesticide spraying in soils and the potential risks for aquatic compartments. Environ. Toxicol. Chem. 2012;31:437-445. (C) 2011 SETAC

A fragment-based approach for ligand binding affinity and selectivity for the liver X receptor beta

Selective modulation of liver X receptor beta (LXR beta) has been recognized as an important approach to prevent or reverse the atherosclerotic process. In the present work, we have developed robust conformation-independent fragment-based quantitative structure-activity and structure-selectivity relationship models for a series of quinolines and cinnolines as potent modulators of the two LXR sub-types. The generated models were then used to predict the potency of an external test set and the predicted values were in good agreement with the experimental results, indicating the potential of the models for untested compounds. The final 2D molecular recognition patterns obtained were integrated to 3D structure-based molecular modeling studies to provide useful insights into the chemical and structural determinants for increased LXR beta binding affinity and selectivity. (C) 2011 Elsevier Inc. All rights reserved.

Computational framework to support integration of biomolecular and clinical data within a translational approach

Background The use of the knowledge produced by sciences to promote human health is the main goal of translational medicine. To make it feasible we need computational methods to handle the large amount of information that arises from bench to bedside and to deal with its heterogeneity. A computational challenge that must be faced is to promote the integration of clinical, socio-demographic and biological data. In this effort, ontologies play an essential role as a powerful artifact for knowledge representation. Chado is a modular ontology-oriented database model that gained popularity due to its robustness and flexibility as a generic platform to store biological data; however it lacks supporting representation of clinical and socio-demographic information. Results We have implemented an extension of Chado – the Clinical Module - to allow the representation of this kind of information. Our approach consists of a framework for data integration through the use of a common reference ontology. The design of this framework has four levels: data level, to store the data; semantic level, to integrate and standardize the data by the use of ontologies; application level, to manage clinical databases, ontologies and data integration process; and web interface level, to allow interaction between the user and the system. The clinical module was built based on the Entity-Attribute-Value (EAV) model. We also proposed a methodology to migrate data from legacy clinical databases to the integrative framework. A Chado instance was initialized using a relational database management system. The Clinical Module was implemented and the framework was loaded using data from a factual clinical research database. Clinical and demographic data as well as biomaterial data were obtained from patients with tumors of head and neck. We implemented the IPTrans tool that is a complete environment for data migration, which comprises: the construction of a model to describe the legacy clinical data, based on an ontology; the Extraction, Transformation and Load (ETL) process to extract the data from the source clinical database and load it in the Clinical Module of Chado; the development of a web tool and a Bridge Layer to adapt the web tool to Chado, as well as other applications. Conclusions Open-source computational solutions currently available for translational science does not have a model to represent biomolecular information and also are not integrated with the existing bioinformatics tools. On the other hand, existing genomic data models do not represent clinical patient data. A framework was developed to support translational research by integrating biomolecular information coming from different “omics” technologies with patient’s clinical and socio-demographic data. This framework should present some features: flexibility, compression and robustness. The experiments accomplished from a use case demonstrated that the proposed system meets requirements of flexibility and robustness, leading to the desired integration. The Clinical Module can be accessed in http://dcm.ffclrp.usp.br/caib/pg=iptrans webcite.