Alternative splicing enriched cDNA libraries identify breast cancer-associated transcripts

Background: Alternative splicing (AS) is a central mechanism in the generation of genomic complexity and is a major contributor to transcriptome and proteome diversity. Alterations of the splicing process can lead to deregulation of crucial cellular processes and have been associated with a large spectrum of human diseases. Cancer-associated transcripts are potential molecular markers and may contribute to the development of more accurate diagnostic and prognostic methods and also serve as therapeutic targets. Alternative splicing-enriched cDNA libraries have been used to explore the variability generated by alternative splicing. In this study, by combining the use of trapping heteroduplexes and RNA amplification, we developed a powerful approach that enables transcriptome-wide exploration of the AS repertoire for identifying AS variants associated with breast tumor cells modulated by ERBB2 (HER-2/neu) oncogene expression. Results: The human breast cell line (C5.2) and a pool of 5 ERBB2 over-expressing breast tumor samples were used independently for the construction of two AS-enriched libraries. In total, 2,048 partial cDNA sequences were obtained, revealing 214 alternative splicing sequence-enriched tags (ASSETs). A subset with 79 multiple exon ASSETs was compared to public databases and reported 138 different AS events. A high success rate of RT-PCR validation (94.5%) was obtained, and 2 novel AS events were identified. The influence of ERBB2-mediated expression on AS regulation was evaluated by capillary electrophoresis and probe-ligation approaches in two mammary cell lines (Hb4a and C5.2) expressing different levels of ERBB2. The relative expression balance between AS variants from 3 genes was differentially modulated by ERBB2 in this model system. Conclusions: In this study, we presented a method for exploring AS from any RNA source in a transcriptome-wide format, which can be directly easily adapted to next generation sequencers. We identified AS transcripts that were differently modulated by ERBB2-mediated expression and that can be tested as molecular markers for breast cancer. Such a methodology will be useful for completely deciphering the cancer cell transcriptome diversity resulting from AS and for finding more precise molecular markers.

Systematic Management of Variability in UML-based Software Product Lines

This paper presents SMarty, a variability management approach for UML-based software product lines (PL). SMarty is supported by a UML profile, the SMartyProfile, and a process for managing variabilities, the SMartyProcess. SMartyProfile aims at representing variabilities, variation points, and variants in UML models by applying a set of stereotypes. SMartyProcess consists of a set of activities that is systematically executed to trace, identify, and control variabilities in a PL based on SMarty. It also identifies variability implementation mechanisms and analyzes specific product configurations. In addition, a more comprehensive application of SMarty is presented using SEI's Arcade Game Maker PL. An evaluation of SMarty and related work are discussed.

Greenhouse gas emissions from alternative futures of deforestation and agricultural management in the southern Amazon

The Brazilian Amazon is one of the most rapidly developing agricultural areas in the world and represents a potentially large future source of greenhouse gases from land clearing and subsequent agricultural management. In an integrated approach, we estimate the greenhouse gas dynamics of natural ecosystems and agricultural ecosystems after clearing in the context of a future climate. We examine scenarios of deforestation and postclearing land use to estimate the future (2006-2050) impacts on carbon dioxide (CO(2)), methane (CH(4)), and nitrous oxide (N(2)O) emissions from the agricultural frontier state of Mato Grosso, using a process-based biogeochemistry model, the Terrestrial Ecosystems Model (TEM). We estimate a net emission of greenhouse gases from Mato Grosso, ranging from 2.8 to 15.9 Pg CO(2)-equivalents (CO(2)-e) from 2006 to 2050. Deforestation is the largest source of greenhouse gas emissions over this period, but land uses following clearing account for a substantial portion (24-49%) of the net greenhouse gas budget. Due to land-cover and land-use change, there is a small foregone carbon sequestration of 0.2-0.4 Pg CO(2)-e by natural forests and cerrado between 2006 and 2050. Both deforestation and future land-use management play important roles in the net greenhouse gas emissions of this frontier, suggesting that both should be considered in emissions policies. We find that avoided deforestation remains the best strategy for minimizing future greenhouse gas emissions from Mato Grosso.

Changes in soil organic carbon storage under different agricultural management systems in the Southwest Amazon Region of Brazil

The Cerrado and Amazon regions of Brazil are probably the largest agricultural frontier of the world, and Could be a sink or source for C depending on the net effect of land use change and subsequent management on soil organic C pools. We evaluated the effects of agricultural management systems on soil organic C (SOC) stocks in the Brazilian states of Rondonia and Mato Grosso, and derived regional specific factors for soil C stock change associated with different management systems. We used 50 observations (data points) in this study, including 42 dealing with annual cropping practices and 8 dealing with perennial cropping, and analyzed the data in linear mixed-effect models. No tillage (NT) systems in Cerrado areas increased SOC Storage by 1.08 +/- 0.06 relative to SOC stocks under native conditions, while SOC storage increased by a modest factor of 1.01 +/- 0.17 in Cerradao and Amazon Forest conditions. Full tillage (FT) had negative effect on SOC storage relative to NT, decreasing SOC stocks by a factor of 0.94 +/- 0.04. but did not significantly reduce SOC stocks relative to native levels when adopted in the Cerrado region. Perennial cropping had a minimal impact on SOC stocks, estimated at a factor Value of 0.98 +/- 0.14, suggesting these systems maintain about 98% of the SOC stock found under native vegetation. The results Suggest that NT adoption may be increasing SOC with land use change from native vegetation to cropland management in the Cerrado region of Brazil. (C) 2009 Elsevier B.V. All rights reserved.

Effect of grassland management on soil carbon sequestration in Rondonia and Mato Grosso states, Brazil

Grassland management affects soil organic carbon (SOC) content and a variety of management options have been proposed to sequester carbon. However, studies conducted in Brazilian pastures have shown divergent responses for the SOC depending on management practices. Our objective was to evaluate the effects of management on SOC stocks in grasslands of the Brazilian states of Rondonia and Mato Grosso, and to derive region-specific factors for soil C stock change associated with different management conditions. Compared to SOC stocks in native vegetation, degraded grassland management decreased SOC by a factor of 0.91 +/- 0.14, nominal grassland management reduced SOC stock for Oxisols by a relatively small factor of 0.99 +/- 0.08, whereas, SOC storage increased by a factor of 1.24 +/- 0.07 with nominal management for other soil types. Improved grassland management on Oxisols increased SOC storage by 1.19 +/- 0.07, relative to native stocks, but there were insufficient data to evaluate the impact of improved grassland management for other soil types. Using these results, we also evaluated the potential for grassland management to sequester or emit C to the atmosphere, and found that degraded grassland management decreased stocks by about 0.27-0.28 Mg C ha(-1) yr(-1); nominal management on Oxisols decreased C at a rate of 0.03 Mg C ha(-1) yr(-1), while nominal management on others soil types and improved management on Oxisols increased stocks by 0.72 Mg C ha(-1) yr(-1) and 0.61 Mg C ha(-1) yr(-1), respectively. Therefore, when well managed or improved, grasslands in Rondonia and Mato Grosso states have the potential to sequester C. (c) 2008 Elsevier B.V. All rights reserved.

Forest-related partnerships in Brazilian Amazonia: There is more to sustainable forest management than reduced impact logging

There is more to sustainable forest management than reduced impact logging. Partnerships between multiple actors are needed in order to create the institutional context for good forest governance and sustainable forest management and stimulate the necessary local community involvement. The idea behind this is that the parties would be able to achieve more jointly than on their own by combining assets, knowledge, skills and political power of actors at different levels of scale. This article aims to demonstrate by example the nature and variety of forest-related partnerships in Brazilian Amazonia. Based on the lessons learned from these cases and the authors` experience, the principal characteristics of successful partnerships are described, with a focus on political and socioeconomic aspects. These characteristics include fairly negotiated partnership objectives, the active involvement of the public sector as well as impartial brokers, equitable and cost-effective institutional arrangements, sufficient and equitably shared benefits for all the parties involved, addressing socioeconomic drawbacks, and taking measures to maintain sustainable exploitation levels. The authors argue that, in addition to product-oriented partnerships which focus on sustainable forest management, there is also a need for politically oriented partnerships based on civil society coalitions. The watchdog function of these politically oriented partnerships, their awareness-raising campaigns regarding detrimental policies and practices, and advocacy for good forest governance are essential for the creation of the appropriate legal and political framework for sustainable forest management. (C) 2008 Elsevier B.V. All rights reserved.

New perspectives on the processing and release of public information

This article discusses issues related to the organization and reception of information in the context of services and public information systems driven by technology. It stems from the assumption that in a ""technologized"" society, the distance between users and information is almost always of cognitive and socio-cultural nature, a product of our effort to design communication. In this context, we favor the approach of the information sign, seeking to answer how a documentary message turns into information, i.e. a structure recognized as socially useful. Observing the structural, cognitive and communicative aspects of the documentary message, based on Documentary Linguistics, Terminology, as well as on Textual Linguistics, the policy of knowledge management and innovation of the Government of the State of Sao Paulo is analyzed, which authorizes the use of Web 2.0, also questioning to what extent this initiative represents innovation in the environment of libraries.

Brazilian registered nurses` perceptions and attitudes towards adverse events in nursing care: a phenomenological study

Aim To describe the perceptions and attitudes of registered nurses (RNs) towards adverse events (AEs) in nursing care. Background The professionals` subjective perspectives should be taken into account for the prevention of AEs in care settings. Method Schutz`s social phenomenology was developed. Interviews were conducted with nine Intensive Care Unit RNs. Results The following five descriptive categories emerged: (1) the occurrence of AEs is inherent to the human condition but provokes a feeling of insecurity, (2) the occurrence of AEs indicates the existence of failures in health care systematization, (3) the professionals` attitudes towards AEs should be permeated by ethical principles; (4) the priority regarding AEs should be the mitigation of harm to patients, and (5) decisions regarding the communication of AEs were determined by the severity of the error. Conclusions The various subjective perspectives related to the occurrence of AEs requires a health care systematization with a focus on prevention. Ethical behaviour is essential for the patients` safety. Implications for nursing management Activities aimed at the prevention of AEs should be integrated jointly with both the professionals and the health care institution. A culture of safety, not punishment, and improvement in the quality of care provided to patients should be priorities.

Nasopharyngeal Intubation in Robin Sequence: Technique and Management

Objective: To provide a detailed description of the nasopharyngeal intubation (NPI) technique and photographs, which should be helpful for those who may need to perform it for treating the airway obstruction in Robin sequence. Design: To describe and illustrate the NPI technique and the necessary considerations for its application. Setting: Hospital de Reabilitacao de Anomalias Craniofacial of University of Sao Paulo, Brazil. Result: The NPI procedure involves the use of a whitish, Portex, number 3.0 or 3.5, silicone tube, introduced 8 cm deep into the infant`s nostril and fixed with Micropore tape. The tube is to be removed at least twice a day for proper hygiene (with running water, detergent, and swabs) and should be changed every 7 days. This procedure is taught to the children`s parents or caretakers by the nurse during hospitalization. Conclusion: The technique is so simple that it can be performed by the parents themselves, allowing continuation of the treatment at home.

Acute effects and postactivation potentiation in the special judo fitness test

Miarka, B, Del Vecchio, FB, and Franchini, E. Acute effects and postactivation potentiation in the special judo fitness test. J Strength Cond Res 25(2): 427-431, 2011-The purpose of this study was to compare the acute short-term effects of (1) plyometric exercise, (2) combined strength and plyometric exercise (contrast), and (3) maximum strength performance in the Special Judo Fitness Test (SJFT). Eight male judo athletes (mean +/- SD, age, 19 +/- 1 years; body mass, 60.4 +/- 5 kg; height, 168.3 +/- 5.4 cm) took part in this study. Four different sessions were completed; each session had 1 type of intervention: (a) SJFT control, (b) plyometric exercises + SJFT, (c) maximum strength + SJFT, and (d) contrast + SJFT. The following variables were quantified: throws performed during series A, B, and C; total number of throws; heart rate immediately and 1 minute after the test; and test index. Significant differences were found in the number of throws during series A: the plyometric exercise (6.4 +/- 0.5 throws) was superior (p < 0.05) to the control condition (5.6 +/- 0.5 throws). Heart rate 1 minute after the SJFT was higher (p < 0.01) during the plyometric exercise (192 +/- 8 bpm) than during the contrast exercise (184 +/- 9 bpm). The contrast exercise (13.58 +/- 0.72) resulted in better index values than the control (14.67 +/- 1.30) and plyometric exercises (14.51 +/- 0.54). Thus, this study suggests that contrast and plyometric exercises performed before the SJFT can result in improvements in the test index and anaerobic power of judo athletes, respectively.

A special judo fitness test classificatory table

Background and Study Aim: Judo is very physiological demanding sport, but there are no many physical fitness specific tests. One of the most used specific judo tests is the Special Judo Fitness Test (SJFT) proposed by Sterkowicz ( 1995). Although this test has been used by many coaches in different countries no classificatory table was found to classify the judo athletes according to their results. Thus, the aim of this work was to present a classificatory table for this test. Material/Methods: For this purpose 141 judo athletes ( mean +/-standard deviation: 21.3+/-4.5years-old; 74.2+/-15.9 kg of body mass and 176.7+/-8.2 cm of height; judo ranking between 3(rd) kyu and 3(rd) dan) familiarized with the SJFT performed it once in order to provide data to establish a classificatory table. Results: After the analysis of data distribution a five scale table (20% for each classificatory category) was developed considering the variables used in the SJFT ( number of throws, heart rate after and 1 min after the test and index). Conclusions: The classificatory table can help coaches using the SJFT to classify their athletes` level and to monitor their physical fitness progress.

Regulating industrial forest concessions in Central Africa and South America

Tropical countries face special specific problems in implementing sustainable forest management (SFM). In many countries, questions are raised on whether tropical forests should be publicly, commonly or privately owned and managed in order to enhance sustainability. Other debates also focus on whether small-scale enterprises are better positioned than large-scale industrial concessions to reduce poverty and attain sustainable management. In countries where large tracts of forest are state-owned, concessions are viewed as a means of delivering services of public and collective interest through an association of private investment and public regulation. However, the success of an industrial concession model in countries with large forest resource endowment to achieve multiple goals such as sustainable forest management and local/regional development depends on two critical assumptions. First, forest functions and services should be managed and maintained as public goods. In many cases, additional uses - and corresponding rights - can take place alongside logging activities. Industrial concessions can be more efficient than other tenure models (such as community-based forest management and small-scale enterprises) in achieving SFM, add value to raw material and comply with growing environmental norms. This is especially the case in market-remote areas with low population density and poor infrastructure. Secondly, to achieve these different outcomes, any concession system needs to be monitored and regulated, especially in contexts dominated by asymmetrical information between regulating authorities and concessionaires. New institutional responses have recently been put forward in several countries, providing valuable materials to design a renewed policy mix which associates public and private incentives. This paper provides a survey of the experience of forest concessions in several Central African and South American countries. The concession system is examined in order to clarify the issues involved, the problems encountered, and what can be learned from the shared experience of these countries in the last decade. This paper argues that despite a sometimes patchy record, concessions can help promote SFM so long as they are packaged with a certain number of specific measures. (C) 2008 Elsevier B.V. All rights reserved.

Ecodesign methods focused on remanufacturing

Understanding the product`s `end-of-life` is important to reduce the environmental impact of the products` final disposal. When the initial stages of product development consider end-of-life aspects, which can be established by ecodesign (a proactive approach of environmental management that aims to reduce the total environmental impact of products), it becomes easier to close the loop of materials. The `end-of-life` ecodesign methods generally include more than one `end-of-life` strategy. Since product complexity varies substantially, some components, systems or sub-systems are easier to be recycled, reused or remanufactured than others. Remanufacture is an effective way to maintain products in a closed-loop, reducing both environmental impacts and costs of the manufacturing processes. This paper presents some ecodesign methods focused on the integration of different `end-of-life` strategies, with special attention to remanufacturing, given its increasing importance in the international scenario to reduce the life cycle impacts of products. (C) 2009 Elsevier Ltd. All rights reserved.

The central role of human resource management in the search for sustainable organizations

The aim of this article is to present the main contributions of human resource management to develop sustainable organizations. The relationship between human resources and organizational sustainability, which is based on economical, social and environmental performance, involves some important aspects concerning management such as innovation, cultural diversity and the environment. The integration of items from the triple bottom line approach leads to developing a model based on a strategic and central posture of human resource management. Based on this model, propositions and recommendations for future research on this theme are presented.

Environmental management system and human resource practices: is there a link between them in four Brazilian companies?

The aim of this article is to analyze the theoretical model proposed by [Jabbour CJC, Santos FCA. Relationships between human resource dimensions and environmental management in companies: proposal of a model. Journal of Cleaner Production 2008;16(1):5 1-8.] based on the data collected in four Brazilian companies. This model investigates how the phases of the environmental management system can be linked to human resource practices in order to attain continuous improvement of a company`s environmental performance. Our aim is to contribute to a field, which has little empirical evidence. Although the interaction between the phases of the environmental management system and human resource practices is recommended by the specialized literature [Daily BE Huang S. Achieving sustainability through attention to human resource factors in environmental management. International Journal of Operations and Production Management 2001:21(12):1539-52.], the results indicate that most of the theoretical assumptions could not be confirmed in these Brazilian companies. (C) 2008 Elsevier Ltd. All rights reserved.