Survival, Causes of Death, and Prognostic Factors in Systemic Sclerosis: Analysis of 947 Brazilian Patients

Objective. To analyze survival, prognostic factors, and causes of death in a large cohort of patients with systemic sclerosis (SSc). Methods. From 1991 to 2010, 947 patients with SSc were treated at 2 referral university centers in Brazil. Causes of death were considered SSc-related and non-SSc-related. Multiple logistic regression analysis was used to identify prognostic factors. Survival at 5 and 10 years was estimated using the Kaplan-Meier method. Results. One hundred sixty-eight patients died during the followup. Among the 110 deaths considered related to SSc, there was predominance of lung (48.1%) and heart (24.5%) involvement. Most of the 58 deaths not related to SSc were caused by infection, cardiovascular or cerebrovascular disease, and cancer. Male sex, modified Rodnan skin score (mRSS) > 20, osteoarticular involvement, lung involvement, and renal crisis were the main prognostic factors associated to death. Overall survival rate was 90% for 5 years and 84% for 10 years. Patients presented worse prognosis if they had diffuse SSc (85% vs 92% at 5 yrs, respectively, and 77% vs 87% at 10 yrs, compared to limited SSc), male sex (77% vs 90% at 5 yrs and 64% vs 86% at 10 yrs, compared to female sex), and mRSS > 20 (83% vs 90% at 5 yrs and 66% vs 86% at 10 yrs, compared to mRSS <20). Conclusion. Survival was worse in male patients with diffuse SSc, and lung and heart involvement represented the main causes of death in this South American series of patients with SSc. (First Release Aug 15 2012; J Rheumatol 2012;39:1971-8; doi:10.3899/jrheum.111582)

How far can we go in simplifying biomonitoring assessments? An integrated analysis of taxonomic surrogacy, taxonomic sufficiency and numerical resolution in a megadiverse region

The need for biodiversity conservation is increasing at a rate much faster than the acquisition of knowledge of biodiversity, such as descriptions of new species and mapping species distributions. As global changes are winning the race against the acquisition of knowledge, many researchers resort to the use of surrogate groups to aid in conservation decisions. Reductions in taxonomic and numerical resolution are also desirable, because they could allow more rapid the acquisition of knowledge while requiring less effort, if little important information is lost. In this study, we evaluated the congruence among 22 taxonomic groups sampled in a tropical forest in the Amazon basin. Our aim was to evaluate if any of these groups could be used as surrogates for the others in monitoring programs. We also evaluated if the taxonomic or numerical resolution of possible surrogates could be reduced without greatly reducing the overall congruence. Congruence among plant groups was high, whereas the congruence among most animal groups was very low, except for anurans in which congruence values were only slightly lower than for plants. Liana (Bignoniaceae) was the group with highest congruence, even using genera presence-absence data. The congruence among groups was related to environmental factors, specifically the clay and phosphorous contents of soil. Several groups showed strong spatial clumping, but this was unrelated to the congruence among groups. The high degree of congruence of lianas with the other groups suggests that it may be a reasonable surrogate group, mainly for the other plant groups analyzed, if soil data are not available. Although lianas are difficult to count and identify, the number of studies on the ecology of lianas is increasing. Most of these studies have concluded that lianas are increasing in abundance in tropical forests. In addition to the high congruence, lianas are worth monitoring in their own right because they are sensitive to global warming and the increasing frequency and severity of droughts in tropical regions. Our findings suggest that the use of data on surrogate groups with relatively low taxonomic and numerical resolutions can be a reliable shortcut for biodiversity assessments, especially in megadiverse areas with high rates of habitat conversion, where the lack of biodiversity knowledge is pervasive. (c) 2012 Elsevier Ltd. All rights reserved.

Integrated landmark and outline-based morphometric methods efficiently distinguish species of Euglossa (Hymenoptera, Apidae, Euglossini)

Morphometric methods permit identification of insect species and are an aid for taxonomy. Quantitative wing traits were used to identify male euglossine bees. Landmark- and outline-based methods have been primarily used independently. Here, we combine the two methods using five Euglossa. Landmark-based methods correctly classified 84% and outline-based 77%, but an integrated analysis correctly classified 91% of samples. Some species presented significantly high reclassification percentages when only wing cell contour was considered, and correct identification of specimens with damaged wings was also obtained using this methodology.

Semantic integration of gene expression analysis tools and data sources using software connectors

Abstract Background The study and analysis of gene expression measurements is the primary focus of functional genomics. Once expression data is available, biologists are faced with the task of extracting (new) knowledge associated to the underlying biological phenomenon. Most often, in order to perform this task, biologists execute a number of analysis activities on the available gene expression dataset rather than a single analysis activity. The integration of heteregeneous tools and data sources to create an integrated analysis environment represents a challenging and error-prone task. Semantic integration enables the assignment of unambiguous meanings to data shared among different applications in an integrated environment, allowing the exchange of data in a semantically consistent and meaningful way. This work aims at developing an ontology-based methodology for the semantic integration of gene expression analysis tools and data sources. The proposed methodology relies on software connectors to support not only the access to heterogeneous data sources but also the definition of transformation rules on exchanged data. Results We have studied the different challenges involved in the integration of computer systems and the role software connectors play in this task. We have also studied a number of gene expression technologies, analysis tools and related ontologies in order to devise basic integration scenarios and propose a reference ontology for the gene expression domain. Then, we have defined a number of activities and associated guidelines to prescribe how the development of connectors should be carried out. Finally, we have applied the proposed methodology in the construction of three different integration scenarios involving the use of different tools for the analysis of different types of gene expression data. Conclusions The proposed methodology facilitates the development of connectors capable of semantically integrating different gene expression analysis tools and data sources. The methodology can be used in the development of connectors supporting both simple and nontrivial processing requirements, thus assuring accurate data exchange and information interpretation from exchanged data.

Physical-chemical and microbiological changes in Cerrado Soil under differing sugarcane harvest management systems

Background: Sugarcane cultivation plays an important role in Brazilian economy, and it is expanding fast, mainly due to the increasing demand for ethanol production. In order to understand the impact of sugarcane cultivation and management, we studied sugarcane under different management regimes (pre-harvest burn and mechanical, unburnt harvest, or green cane), next to a control treatment with native vegetation. The soil bacterial community structure (including an evaluation of the diversity of the ammonia oxidizing (amoA) and denitrifying (nirK) genes), greenhouse gas flow and several soil physicochemical properties were evaluated. Results: Our results indicate that sugarcane cultivation in this region resulted in changes in several soil properties. Moreover, such changes are reflected in the soil microbiota. No significant influence of soil management on greenhouse gas fluxes was found. However, we did find a relationship between the biological changes and the dynamics of soil nutrients. In particular, the burnt cane and green cane treatments had distinct modifications. There were significant differences in the structure of the total bacterial, the ammonia oxidizing and the denitrifying bacterial communities, being that these groups responded differently to the changes in the soil. A combination of physical and chemical factors was correlated to the changes in the structures of the total bacterial communities of the soil. The changes in the structures of the functional groups follow a different pattern than the physicochemical variables. The latter might indicate a strong influence of interactions among different bacterial groups in the N cycle, emphasizing the importance of biological factors in the structuring of these communities. Conclusion: Sugarcane land use significantly impacted the structure of total selected soil bacterial communities and ammonia oxidizing and denitrifier gene diversities in a Cerrado field site in Central Brazil. A high impact of land use was observed in soil under the common burnt cane management. The green cane soil also presented different profiles compared to the control soil, but to at a lesser degree.

An integrated GIS for sedimentological and geomorphological analysis of a lagoon environment. Barra de Cananeia inlet region, (Southeastern Brazil)

The aim of this work is to use GIS integration data to characterize sedimentary processes in a SubTropical lagoon environment. The study area was the Canan,ia Inlet estuary in the southeastern section of the Canan,ia Lagoon Estuarine System (CLES), state of So Paulo, Brazil (25A degrees 03'S/47A degrees 53'W). The area is formed by the confluence of two estuarine channels forming a bay-shaped water body locally called "Trapand, Bay". The region is surrounded by one of the most preserved tracts of Atlantic Rain Forest in Southwestern Brazil and presents well-developed mangroves and marshes. In this study a methodology was developed using integrated a GIS database based on bottom sediment parameters, geomorphological data, remote sensing images, Hidrodynamical Modeling data and geophysical parameters. The sediment grain size parameters and the bottom morphology of the lagoon were also used to develop models of net sediment transport pathways. It was possible to observe that the sediment transport vectors based on the grain size model had a good correlation with the transport model based on the bottom topography features and Hydrodynamic model, especially in areas with stronger energetic conditions, with a minor contribution of finer sediments. This relation is somewhat less evident near shallower banks and depositional features. In these regions the organic matter contents in the sediments was a good complementary tool for inferring the hydrodynamic and depositional conditions (i.e. primary productivity, sedimentation rates, sources, oxi-reduction rates).

Extensive cross-talk and global regulators identified from an analysis of the integrated transcriptional and signaling network in Escherichia coli

To understand the regulatory dynamics of transcription factors (TFs) and their interplay with other cellular components we have integrated transcriptional, protein-protein and the allosteric or equivalent interactions which mediate the physiological activity of TFs in Escherichia coli. To study this integrated network we computed a set of network measurements followed by principal component analysis (PCA), investigated the correlations between network structure and dynamics, and carried out a procedure for motif detection. In particular, we show that outliers identified in the integrated network based on their network properties correspond to previously characterized global transcriptional regulators. Furthermore, outliers are highly and widely expressed across conditions, thus supporting their global nature in controlling many genes in the cell. Motifs revealed that TFs not only interact physically with each other but also obtain feedback from signals delivered by signaling proteins supporting the extensive cross-talk between different types of networks. Our analysis can lead to the development of a general framework for detecting and understanding global regulatory factors in regulatory networks and reinforces the importance of integrating multiple types of interactions in underpinning the interrelationships between them.

Analysis of genetic lineages and their correlation with virulence genes in enterococcus faecalis clinical isolates from root canal and systemic infections

Introduction: Enterococcus faecalis is a member of the mammalian gastrointestinal microbiota but has been considered a leading cause of hospital-acquired infections. In the oral cavity, it is commonly detected from root canals of teeth with failed endodontic treatment. However, little is known about the virulence and genetic relatedness among E. faecalis isolates from different clinical sources. This study compared the presence of enterococcal virulence factors among root canal strains and clinical isolates from hospitalized patients to identify virulent clusters of E. faecalis. Methods: Multilocus sequence typing analysis was used to determine genetic lineages of 40 E. faecalis clinical isolates from different sources. Virulence clusters were determined by evaluating capsule (cps) locus polymorphisms, pathogenicity island gene content, and antibiotic resistance genes by polymerase chain reaction. Results: The clinical isolates from hospitalized patients formed a phylogenetically separate group and were mostly grouped in the clonal complex 2, which is a known virulent cluster of E. faecalis that has caused infection outbreaks globally. The clonal complex 2 group comprised capsule-producing strains harboring multiple antibiotic resistance and pathogenicity island genes. On the other hand, the endodontic isolates were more diverse and harbored few virulence and antibiotic resistance genes. In particular, although more closely related to isolates from hospitalized patients, capsuleproducing E. faecalis strains from root canals did not carry more virulence/antibiotic genes than other endodontic isolates. Conclusions: E. faecalis isolates from endodontic infections have a genetic and virulence profile different from pathogenic clusters of hospitalized patients’ isolates, which is most likely due to niche specialization conferred mainly by variable regions in the genome.

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.

AcMus: an Open, Integrated Platform for Room Acoustics Research

This article describes the design, implementation, and experiences with AcMus, an open and integrated software platform for room acoustics research, which comprises tools for measurement, analysis, and simulation of rooms for music listening and production. Through use of affordable hardware, such as laptops, consumer audio interfaces and microphones, the software allows evaluation of relevant acoustical parameters with stable and consistent results, thus providing valuable information in the diagnosis of acoustical problems, as well as the possibility of simulating modifications in the room through analytical models. The system is open-source and based on a flexible and extensible Java plug-in framework, allowing for cross-platform portability, accessibility and experimentation, thus fostering collaboration of users, developers and researchers in the field of room acoustics.

Paleoenvironmental reconstruction of a Late Quaternary lagoon system in southern Brazil (Jaguaruna region, Santa Catarina state) based on multi-proxy analysis

This paper provides a paleoenvironmental reconstruction of a Late Quaternary lagoon system in the Jaguaruna region of Santa Catarina state, southern Brazil. Integrated results of bulk sedimentary organic matter characterization (delta C-13, delta N-15 and C/N), microfossil (pollen and diatom) and grain-size analysis from three shallow cores (similar to 2.5m depth) allowed us to propose an evolving paleogeographic scenario in this coastal region for the last ca. 5500 cal a BP. The lagoonal system in this area was more extensive during the mid-Holocene than today, with a gradual and continuous lagoon-sea disconnection until the present. We add to the debate regarding relative sea-level (RSL) variations for the Brazilian coast during the Holocene and discuss the importance of sedimentary dynamics for interpreting changes in coastal ecosystems. The multi-proxy analysis suggests that changes in coastal ecosystems could be directly related to local sedimentary processes, which are not necessarily linked to RSL fluctuations and/or to climatic variations. Copyright (c) 2011 John Wiley & Sons, Ltd.

A mixed model QTL analysis for sugarcane multiple-harvest-location trial data

Sugarcane-breeding programs take at least 12 years to develop new commercial cultivars. Molecular markers offer a possibility to study the genetic architecture of quantitative traits in sugarcane, and they may be used in marker-assisted selection to speed up artificial selection. Although the performance of sugarcane progenies in breeding programs are commonly evaluated across a range of locations and harvest years, many of the QTL detection methods ignore two- and three-way interactions between QTL, harvest, and location. In this work, a strategy for QTL detection in multi-harvest-location trial data, based on interval mapping and mixed models, is proposed and applied to map QTL effects on a segregating progeny from a biparental cross of pre-commercial Brazilian cultivars, evaluated at two locations and three consecutive harvest years for cane yield (tonnes per hectare), sugar yield (tonnes per hectare), fiber percent, and sucrose content. In the mixed model, we have included appropriate (co)variance structures for modeling heterogeneity and correlation of genetic effects and non-genetic residual effects. Forty-six QTLs were found: 13 QTLs for cane yield, 14 for sugar yield, 11 for fiber percent, and 8 for sucrose content. In addition, QTL by harvest, QTL by location, and QTL by harvest by location interaction effects were significant for all evaluated traits (30 QTLs showed some interaction, and 16 none). Our results contribute to a better understanding of the genetic architecture of complex traits related to biomass production and sucrose content in sugarcane.

Increased IgE serum levels are unrelated to allergic and parasitic diseases in patients with juvenile systemic lupus erythematosus

OBJECTIVE: The aim of this study was to assess the IgE serum levels in juvenile systemic lupus erythematosus patients and to evaluate possible associations with clinical and laboratory features, disease activity and tissue damage. METHODS: The IgE serum concentrations in 69 consecutive juvenile systemic lupus erythematosus patients were determined by nephelometry. IgG, IgM and IgA concentrations were measured by immunoturbidimetry. All patients were negative for intestinal parasites. Statistical analysis methods included the Mann-Whitney, chi-square and Fisher's exact tests, as well as the Spearman rank correlation coefficient. RESULTS: Increased IgE concentrations above 100 IU/mL were observed in 31/69 (45%) juvenile systemic lupus erythematosus patients. The mean IgE concentration was 442.0 +/- 163.4 IU/ml (range 3.5- 9936.0 IU/ml). Fifteen of the 69 patients had atopic disease, nine patients had severe sepsis and 56 patients presented with nephritis. The mean IgE level in 54 juvenile systemic lupus erythematosus patients without atopic manifestations was 271.6 +/- 699.5 IU/ml, and only nine of the 31 (29%) patients with high IgE levels had atopic disease. The IgE levels did not statistically differ with respect to the presence of atopic disease, severe sepsis, nephritis, disease activity, or tissue damage. Interestingly, IgE concentrations were inversely correlated with C4 levels ( r = -0.25, p = 0.03) and with the SLICC/ACR-DI score (r = -0.34, p = 0.005). The IgE concentration was also found to be directly correlated with IgA levels (r = 0.52, p = 0.03). CONCLUSIONS: The present study demonstrated for the first time that juvenile systemic lupus erythematosus patients have increased IgE serum levels. This increase in IgE levels was not related to allergic or parasitic diseases. Our results are in line with the hypothesis that high IgE levels can be considered a marker of immune dysregulation.

Tragedy on grade crossing: driver failure or systemic fragility?

In 2010, an accident occurred in Americana-SP, Brazil, involving two trains and one bus on a Grade Crossing, when 10 people died and 17 were injured including workers. This paper aims to analyze the accident using the Model of Analysis and Prevention of Work Accidents (MAPA). The method provides observation of work, interviews and analysis of documents to understand precedents of the event in the following stages: to understand the usual work from the involved people, the changes occurred in the system, the operation of barriers, managerial and organizational aspects. By the end, measures are suggested to avoid new occurrences. The accident took place at night in a site with insufficient lighting. The working conditions of bus drivers, train operators and watchmen are inadequate. There were only symbolic barriers (visual and acoustic signals) triggered manually by watchman upon train operator radio communication. The fragility of the barrier system associated to poor lighting and short time to trigger the signaling seem to play a critical role in the event. Contrary to the official report which resulted in guilt of the bus driver, the conclusion of the paper emphasizes the fragility of the safety system and the need of level crossing reproject.