'Diabetology & Metabolic Syndrome: providing an open access future for diabetes research'

Diabetology & Metabolic Syndrome (D&MS), the official journal of the Brazilian Diabetes Society (SBD), is a new open access, peer reviewed journal publishing research on all aspects of the pathophysiology of diabetes and metabolic syndrome. With the many ongoing and upcoming challenges for diabetes diagnosis, treatment and care, a dedicated journal providing unrestricted access for researchers and health care professionals working in the field of diabetes is needed. Diabetology & Metabolic Syndrome aims to fulfil this need.

White paper sobre Open Source, Open Access, open Standards e o futuro da catalogação

The discussions on the future of cataloging has received increased attention in the last ten years, mainly due to the impact of rapid development of information and communication technologies in the same period, which has provided access to the Web anytime, anywhere. These discussions revolve around the need for a new bibliographic framework to meet the demand of this new reality in the digital environment, ie how libraries can process, store, deliver, share and integrate their collections (physical, digital or scanned), in current post-PC era? Faced with this question, Open Access, Open Source and Open Standards are three concepts that need to receive greater attention in the field of Library and Information Science, as it is believed to be fundamental elements for the change of paradigm of descriptive representation, currently based conceptually on physical item rather than intellectual work. This paper aims to raise and discuss such issues and instigate information professionals, especially librarians, to think, discuss and propose initiatives for such problems, contributing and sharing ideas and possible solutions, in multidisciplinary teams. At the end is suggested the effective creation of multidisciplinary and inter-institutional study groups on the future of cataloging and its impact on national collections, in order to contribute to the area of descriptive representation in national and international level

Digital library of historical cartography: open access to cultural heritage and public good

This paper describes the integration of information between Digital Library of Historical Cartography and Bibliographical Database (DEDALUS), both of the University of São Paulo (USP), to guarantee open, public access by Internet to the maps in the collection and make them available to users everywhere. This digital library was designed by Historical Cartography Studies Laboratory team (LECH/USP), and provides maps images on the Web, of high resolution, as well as such information on these maps as technical-scientific data (projection, scale, coordinates), printing techniques and material support that have made their circulation and cultural consumption possible. The Digital Library of Historical Cartography is accessible not only to the historical cartography researchers, but also to students and the general public. Beyond being a source of information about maps, the Digital Library of Historical Cartography seeks to be interactive, exchanging information and seeking dialogue with different branches of knowledge

University of São Paulo, Brazil: open access movement

USP scientific production. USP journals. USP Open Access Movement.

A resource management scenario for traditional and scientific management of pink shrimp (Farfantepenaeus paulensis) in the Patos Lagoon estuary (RS), Brazil

Abstract Background This article aims to discuss the incorporation of traditional time in the construction of a management scenario for pink shrimp in the Patos Lagoon estuary (RS), Brazil. To meet this objective, two procedures have been adopted; one at a conceptual level and another at a methodological level. At the conceptual level, the concept of traditional time as a form of traditional ecological knowledge (TEK) was adopted. Method At the methodological level, we conduct a wide literature review of the scientific knowledge (SK) that guides recommendations for pink shrimp management by restricting the fishing season in the Patos Lagoon estuary; in addition, we review the ethno-scientific literature which describes traditional calendars as a management base for artisanal fishers in the Patos Lagoon estuary. Results Results demonstrate that TEK and SK describe similar estuarine biological processes, but are incommensurable at a resource management level. On the other hand, the construction of a “management scenario” for pink shrimp is possible through the development of “criteria for hierarchies of validity” which arise from a productive dialog between SK and TEK. Conclusions The commensurable and the incommensurable levels reveal different basis of time-space perceptions between traditional ecological knowledge and scientific knowledge. Despite incommensurability at the management level, it is possible to establish guidelines for the construction of “management scenarios” and to support a co-management process.

A comparative transcriptome analysis reveals expression profiles conserved across three Eimeria spp. of domestic fowl and associated with multiple developmental stages

Coccidiosis of the domestic fowl is a worldwide disease caused by seven species of protozoan parasites of the genus Eimeria. The genome of the model species, Eimeria tenella, presents a complexity of 55-60 MB distributed in 14 chromosomes. Relatively few studies have been undertaken to unravel the complexity of the transcriptome of Eimeria parasites. We report here the generation of more than 45,000 open reading frame expressed sequence tag (ORESTES) cDNA reads of E. tenella, Eimeria maxima and Eimeria acervulina, covering several developmental stages: unsporulated oocysts, sporoblastic oocysts, sporulated oocysts, sporozoites and second generation merozoites. All reads were assembled to constitute gene indices and submitted to a comprehensive functional annotation pipeline. In the case of E. tenella, we also incorporated publicly available ESTs to generate an integrated body of information. Orthology analyses have identified genes conserved across different apicomplexan parasites, as well as genes restricted to the genus Eimeria. Digital expression profiles obtained from ORESTES/EST countings, submitted to clustering analyses, revealed a high conservation pattern across the three Eimeria spp. Distance trees showed that unsporulated and sporoblastic oocysts constitute a distinct clade in all species, with sporulated oocysts forming a more external branch. This latter stage also shows a close relationship with sporozoites, whereas first and second generation merozoites are more closely related to each other than to sporozoites. The profiles were unambiguously associated with the distinct developmental stages and strongly correlated with the order of the stages in the parasite life cycle. Finally, we present The Eimeria Transcript Database (http://www.coccidia.icb.usp.br/eimeriatdb), a website that provides open access to all sequencing data, annotation and comparative analysis. We expect this repository to represent a useful resource to the Eimeria scientific community, helping to define potential candidates for the development of new strategies to control coccidiosis of the domestic fowl. (C) 2011 Australian Society for Parasitology Inc. Published by Elsevier Ltd. All rights reserved.

The use of Open Reading frame ESTs (ORESTES) for analysis of the honey bee transcriptome

Abstract Background The ongoing efforts to sequence the honey bee genome require additional initiatives to define its transcriptome. Towards this end, we employed the Open Reading frame ESTs (ORESTES) strategy to generate profiles for the life cycle of Apis mellifera workers. Results Of the 5,021 ORESTES, 35.2% matched with previously deposited Apis ESTs. The analysis of the remaining sequences defined a set of putative orthologs whose majority had their best-match hits with Anopheles and Drosophila genes. CAP3 assembly of the Apis ORESTES with the already existing 15,500 Apis ESTs generated 3,408 contigs. BLASTX comparison of these contigs with protein sets of organisms representing distinct phylogenetic clades revealed a total of 1,629 contigs that Apis mellifera shares with different taxa. Most (41%) represent genes that are in common to all taxa, another 21% are shared between metazoans (Bilateria), and 16% are shared only within the Insecta clade. A set of 23 putative genes presented a best match with human genes, many of which encode factors related to cell signaling/signal transduction. 1,779 contigs (52%) did not match any known sequence. Applying a correction factor deduced from a parallel analysis performed with Drosophila melanogaster ORESTES, we estimate that approximately half of these no-match ESTs contigs (22%) should represent Apis-specific genes. Conclusions The versatile and cost-efficient ORESTES approach produced minilibraries for honey bee life cycle stages. Such information on central gene regions contributes to genome annotation and also lends itself to cross-transcriptome comparisons to reveal evolutionary trends in insect genomes.

Signal transduction-related responses to phytohormones and environmental challenges in sugarcane

Abstract Background Sugarcane is an increasingly economically and environmentally important C4 grass, used for the production of sugar and bioethanol, a low-carbon emission fuel. Sugarcane originated from crosses of Saccharum species and is noted for its unique capacity to accumulate high amounts of sucrose in its stems. Environmental stresses limit enormously sugarcane productivity worldwide. To investigate transcriptome changes in response to environmental inputs that alter yield we used cDNA microarrays to profile expression of 1,545 genes in plants submitted to drought, phosphate starvation, herbivory and N2-fixing endophytic bacteria. We also investigated the response to phytohormones (abscisic acid and methyl jasmonate). The arrayed elements correspond mostly to genes involved in signal transduction, hormone biosynthesis, transcription factors, novel genes and genes corresponding to unknown proteins. Results Adopting an outliers searching method 179 genes with strikingly different expression levels were identified as differentially expressed in at least one of the treatments analysed. Self Organizing Maps were used to cluster the expression profiles of 695 genes that showed a highly correlated expression pattern among replicates. The expression data for 22 genes was evaluated for 36 experimental data points by quantitative RT-PCR indicating a validation rate of 80.5% using three biological experimental replicates. The SUCAST Database was created that provides public access to the data described in this work, linked to tissue expression profiling and the SUCAST gene category and sequence analysis. The SUCAST database also includes a categorization of the sugarcane kinome based on a phylogenetic grouping that included 182 undefined kinases. Conclusion An extensive study on the sugarcane transcriptome was performed. Sugarcane genes responsive to phytohormones and to challenges sugarcane commonly deals with in the field were identified. Additionally, the protein kinases were annotated based on a phylogenetic approach. The experimental design and statistical analysis applied proved robust to unravel genes associated with a diverse array of conditions attributing novel functions to previously unknown or undefined genes. The data consolidated in the SUCAST database resource can guide further studies and be useful for the development of improved sugarcane varieties.

Saphenofemoral arteriovenous fistula as hemodialysis access

Abstract Background An upper limb arteriovenous (AV) fistula is the access of choice for haemodialysis (HD). There have been few reports of saphenofemoral AV fistulas (SFAVF) over the last 10-20 years because of previous suggestions of poor patencies and needling difficulties. Here, we describe our clinical experience with SFAVF. Methods SFAVFs were evaluated using the following variables: immediate results, early and late complications, intraoperative and postoperative complications (up to day 30), efficiency of the fistula after the onset of needling and complications associated to its use. Results Fifty-six SFAVF fistulas were created in 48 patients. Eight patients had two fistulas: 8 patent (16%), 10 transplanted (20%), 12 deaths (24%), 1 low flow (2%) and 20 thrombosis (39%) (first two months of preparation). One patient had severe hypotension during surgery, which caused thrombosis of the fistula, which was successfully thrombectomised, four thrombosed fistulae were successfully thrombectomised and revised on the first postoperative day. After 59 months of follow-up, primary patency was 44%. Conclusion SFAVF is an adequate alternative for patients without the possibility for other access in the upper limbs, allowing efficient dialysis with good long-term patency with a low complication rate.

Pilot survey of expressed sequence tags (ESTs) from the asexual blood stages of Plasmodium vivax in human patients

Abstract Background Plasmodium vivax is the most widely distributed human malaria, responsible for 70–80 million clinical cases each year and large socio-economical burdens for countries such as Brazil where it is the most prevalent species. Unfortunately, due to the impossibility of growing this parasite in continuous in vitro culture, research on P. vivax remains largely neglected. Methods A pilot survey of expressed sequence tags (ESTs) from the asexual blood stages of P. vivax was performed. To do so, 1,184 clones from a cDNA library constructed with parasites obtained from 10 different human patients in the Brazilian Amazon were sequenced. Sequences were automatedly processed to remove contaminants and low quality reads. A total of 806 sequences with an average length of 586 bp met such criteria and their clustering revealed 666 distinct events. The consensus sequence of each cluster and the unique sequences of the singlets were used in similarity searches against different databases that included P. vivax, Plasmodium falciparum, Plasmodium yoelii, Plasmodium knowlesi, Apicomplexa and the GenBank non-redundant database. An E-value of <10-30 was used to define a significant database match. ESTs were manually assigned a gene ontology (GO) terminology Results A total of 769 ESTs could be assigned a putative identity based upon sequence similarity to known proteins in GenBank. Moreover, 292 ESTs were annotated and a GO terminology was assigned to 164 of them. Conclusion These are the first ESTs reported for P. vivax and, as such, they represent a valuable resource to assist in the annotation of the P. vivax genome currently being sequenced. Moreover, since the GC-content of the P. vivax genome is strikingly different from that of P. falciparum, these ESTs will help in the validation of gene predictions for P. vivax and to create a gene index of this malaria parasite.

Hurdles at work: perceptions of hospital food handlers

Abstract Background Food handlers have a very important role in preventing food contamination during its preparation and distribution. This responsibility is even greater in hospitals, since a large number of patients have low immunity and consequently food contamination by pathogenic bacteria could be particularly harmful. Therefore, a good working environment and periodic training should be provided to food handlers by upper management. Methods This study is qualitative research by means of focus group and thematic content analysis methodologies to examine, in detail, the statements by food handlers working in the milk and specific-diet kitchens in a hospital to understand the problems they face in the workplace. Results We found that food handlers are aware of the role they play in restoring patients' health; they consider it important to offer a good-quality diet. However, according to their perceptions, a number of difficulties prevent them from reaching this aim. These include: upper management not prioritizing human and material resources to the dietetic services when making resource allocation decisions; a perception that upper management considers their work to be of lesser importance; delayed overtime payments; lack of periodic training; managers lacking administrative skills; insufficient dietitian staff assistants, leading to overwork, at the same time as there is an excess of dietitians; unhealthy environmental working conditions – high temperature, high humidity, loud and constant noise level, poor ventilation; lack of food, and kitchen utensils and equipment; and relationship conflicts with chief dieticians and co-workers. Conclusion From these findings, improvement in staff motivation could be achieved by considering non-financial incentives, such as improvement in working conditions and showing appreciation and respect through supervision, training and performance appraisal. Management action, such as investments in intermediary management so that managers have the capacity to provide supportive supervision, as well as better use of performance appraisal and access to training, may help overcome the identified problems.

Guidelines for the Development of Comprehensive Care Centers for Congenital Adrenal Hyperplasia: Guidance from the CARES Foundation Initiative

Patients with rare and complex diseases such as congenital adrenal hyperplasia (CAH) often receive fragmented and inadequate care unless efforts are coordinated among providers. Translating the concepts of the medical home and comprehensive health care for individuals with CAH offers many benefits for the affected individuals and their families. This manuscript represents the recommendations of a 1.5 day meeting held in September 2009 to discuss the ideal goals for comprehensive care centers for newborns, infants, children, adolescents, and adults with CAH. Participants included pediatric endocrinologists, internal medicine and reproductive endocrinologists, pediatric urologists, pediatric surgeons, psychologists, and pediatric endocrine nurse educators. One unique aspect of this meeting was the active participation of individuals personally affected by CAH as patients or parents of patients. Representatives of Health Research and Services Administration (HRSA), New York-Mid-Atlantic Consortium for Genetics and Newborn Screening Services (NYMAC), and National Newborn Screening and Genetics Resource Center (NNSGRC) also participated. Thus, this document should serve as a "roadmap" for the development phases of comprehensive care centers (CCC) for individuals and families affected by CAH.

A light in the shadow: the use of Lucifer Yellow technique to demonstrate nectar reabsorption

Abstract Background Nectar reabsorption is a widely known phenomenon, related to the strategy of resource-recovery and also to maintain the nectar homeostasis at the nectary. The method currently performed to demonstrate nectar being reabsorbed involves the use of radioactive tracers applied to the nectary. Although this method works perfectly, it is complex and requires specific supplies and equipment. Therefore, here we propose an efficient method to obtain a visual demonstration of nectar reabsorption, adapting the use of Lucifer Yellow CH (LYCH), a fluorescent membrane-impermeable dye that can enter the vacuole by endocytosis. Results We applied a LYCH solution to the floral nectary (FN) of Cucurbita pepo L., which is a species known for its ability of nectar reabsorption, and to the extrafloral nectary (EFN) of Passiflora edulis Sims which does not reabsorb the secreted nectar. In all tests performed, we observed that LYCH stained the nectary tissues differentially according to the reabsorption ability of the nectary. The treated FN of C. pepo presented a concentrated fluorescence at the epidermis that decreased at the deeper nectary parenchyma, until reaching the vascular bundles, indicating nectar reabsorption in the flowers of the species. In contrast, treated EFN of P. edulis presented fluorescence only at the cuticle surface, indicating that nectar is not reabsorbed by that particular tissue. Conclusion LYCH is an efficient marker to demonstrate nectar reabsorption.

Challenges for nursing education in Angola: the perception of nurse leaders affiliated with professional education institutions

Background: Angola is one of the African countries with the highest morbidity and mortality rates and a devastating lack of human resources for health, including nursing. The World Health Organization stimulates and takes technical cooperation initiatives for human resource education and training in health and education, with a view to the development of countries in the region. The aim in this study was to identify how nurses affiliated with nursing education institutions perceive the challenges nursing education is facing in Angola. Methods: After consulting the National Directory of Human Resources in Angola, the nurse leaders affiliated with professional nursing education institutions in Angola were invited to participate in the study by email. Data were collected in February 2009 through the focus group technique. The group of participants was focused on the central question: what are the challenges faced for nursing education in your country? To register and understand the information, besides the use of a recorder, the reporters elaborated an interpretative report. Data were coded using content analysis. Results: Fourteen nurses participated in the meeting, most of whom were affiliated with technical nursing education institutions. It was verified that the nurse leaders at technical and higher nursing education institutions in Angola face many challenges, mainly related to the lack of infrastructure, absence of trained human resources, bureaucratic problems to regularize the schools and lack of material resources. On the opposite, the solutions they present are predominantly centered on the valuation of nursing professionals, which implies cultural and attitude changes. Conclusions: Public health education policies need to be established in Angola, including action guidelines that permit effective nursing activities. Professional education institutions need further regularizations and nurses need to be acknowledged as key elements for the qualitative enhancement of health services in the country.

Heritability of physical activity traits in Brazilian families: the Baependi Heart Study

Background It is commonly recognized that physical activity has familial aggregation; however, the genetic influences on physical activity phenotypes are not well characterized. This study aimed to (1) estimate the heritability of physical activity traits in Brazilian families; and (2) investigate whether genetic and environmental variance components contribute differently to the expression of these phenotypes in males and females. Methods The sample that constitutes the Baependi Heart Study is comprised of 1,693 individuals in 95 Brazilian families. The phenotypes were self-reported in a questionnaire based on the WHO-MONICA instrument. Variance component approaches, implemented in the SOLAR (Sequential Oligogenic Linkage Analysis Routines) computer package, were applied to estimate the heritability and to evaluate the heterogeneity of variance components by gender on the studied phenotypes. Results The heritability estimates were intermediate (35%) for weekly physical activity among non-sedentary subjects (weekly PA_NS), and low (9-14%) for sedentarism, weekly physical activity (weekly PA), and level of daily physical activity (daily PA). Significant evidence for heterogeneity in variance components by gender was observed for the sedentarism and weekly PA phenotypes. No significant gender differences in genetic or environmental variance components were observed for the weekly PA_NS trait. The daily PA phenotype was predominantly influenced by environmental factors, with larger effects in males than in females. Conclusions Heritability estimates for physical activity phenotypes in this sample of the Brazilian population were significant in both males and females, and varied from low to intermediate magnitude. Significant evidence for heterogeneity in variance components by gender was observed. These data add to the knowledge of the physical activity traits in the Brazilian study population, and are concordant with the notion of significant biological determination in active behavior.