Identification of novel components of NAD-utilizing metabolic pathways and prediction of their biochemical functions

Nicotinamide adenine dinucleotide (NAD) is a ubiquitous cofactor participating in numerous redox reactions. It is also a substrate for regulatory modifications of proteins and nucleic acids via the addition of ADP-ribose moieties or removal of acyl groups by transfer to ADP-ribose. In this study, we use in-depth sequence, structure and genomic context analysis to uncover new enzymes and substrate-binding proteins in NAD-utilizing metabolic and macromolecular modification systems. We predict that Escherichia coli YbiA and related families of domains from diverse bacteria, eukaryotes, large DNA viruses and single strand RNA viruses are previously unrecognized components of NAD-utilizing pathways that probably operate on ADP-ribose derivatives. Using contextual analysis we show that some of these proteins potentially act in RNA repair, where NAD is used to remove 2'-3' cyclic phosphodiester linkages. Likewise, we predict that another family of YbiA-related enzymes is likely to comprise a novel NAD-dependent ADP-ribosylation system for proteins, in conjunction with a previously unrecognized ADP-ribosyltransferase. A similar ADP-ribosyltransferase is also coupled with MACRO or ADP-ribosylglycohydrolase domain proteins in other related systems, suggesting that all these novel systems are likely to comprise pairs of ADP-ribosylation and ribosylglycohydrolase enzymes analogous to the DraG-DraT system, and a novel group of bacterial polymorphic toxins. We present evidence that some of these coupled ADP-ribosyltransferases/ribosylglycohydrolases are likely to regulate certain restriction modification enzymes in bacteria. The ADP-ribosyltransferases found in these, the bacterial polymorphic toxin and host-directed toxin systems of bacteria such as Waddlia also throw light on the evolution of this fold and the origin of eukaryotic polyADP-ribosyltransferases and NEURL4-like ARTs, which might be involved in centrosomal assembly. We also infer a novel biosynthetic pathway that might be involved in the synthesis of a nicotinate-derived compound in conjunction with an asparagine synthetase and AMPylating peptide ligase. We use the data derived from this analysis to understand the origin and early evolutionary trajectories of key NAD-utilizing enzymes and present targets for future biochemical investigations.

Cost-effectiveness analysis of universal childhood hepatitis A vaccination in Brazil: Regional analyses according to the endemic context

Objective: To To conduct a cost-effectiveness analysis of a universal childhood hepatitis A vaccination program in Brazil. Methods: An age and time-dependent dynamic model was developed to estimate the incidence of hepatitis A for 24 years. The analysis was run separately according to the pattern of regional endemicity, one for South + Southeast (low endemicity) and one for the North + Northeast + Midwest (intermediate endemicity). The decision analysis model compared universal childhood vaccination with current program of vaccinating high risk individuals. Epidemiologic and cost estimates were based on data from a nationwide seroprevalence survey of viral hepatitis, primary data collection, National Health Information Systems and literature. The analysis was conducted from both the health system and societal perspectives. Costs are expressed in 2008 Brazilian currency (Real). Results: A universal immunization program would have a significant impact on disease epidemiology in all regions, resulting in 64% reduction in the number of cases of icteric hepatitis, 59% reduction in deaths for the disease and a 62% decrease of life years lost, in a national perspective. With a vaccine price of R$16.89 (US$7.23) per dose, vaccination against hepatitis A was a cost-saving strategy in the low and intermediate endemicity regions and in Brazil as a whole from both health system and society perspective. Results were most sensitive to the frequency of icteric hepatitis, ambulatory care and vaccine costs. Conclusions: Universal childhood vaccination program against hepatitis A could be a cost-saving strategy in all regions of Brazil. These results are useful for the Brazilian government for vaccine related decisions and for monitoring population impact if the vaccine is included in the National Immunization Program. (C) 2012 Elsevier Ltd. All rights reserved.

Chemistry and Chemical Education Through Text and Image: Analysis of Twentieth Century Textbooks Used in Brazilian Context

Assuming that textbooks give literary expression to cultural and ideological values of a nation or group, we propose the analysis of chemistry textbooks used in Brazilian universities throughout the twentieth century. We analyzed iconographic and textual aspects of 31 textbooks which had significant diffusion in the context of Brazilian universities at that period. As a result of the iconographic analysis, nine categories of images were proposed: (1) laboratory and experimentation, (2) industry and production, (3) graphs and diagrams, (4) illustrations related to daily life, (5) models, (6) illustrations related to the history of science, (7) pictures or diagrams of animal, vegetable or mineral samples, (8) analogies and (9) concepts of physics. The distribution of images among the categories showed a different emphasis in the presentation of chemical content due to a commitment to different conceptions of chemistry over the period. So, we started with chemistry as an experimental science in the early twentieth century, with an emphasis change to the principles of chemistry from the 1950s, culminating in a chemistry of undeniable technological influence. Results showed that reflections not only on the history of science, but on the history of science education, may be useful for the improvement of science education.

Alternative Tasks for the Teaching and the Learning of functions: analysis of an intervention in the High School

In this paper we focus on the application of two mathematical alternative tasks to the teaching and learning of functions with high school students. The tasks were elaborated according to the following methodological approach: (i) Problem Solving and/or mathematics investigation and (ii) a pedagogical proposal, which defends that mathematical knowledge is developed by means of a balance between logic and intuition. We employed a qualitative research approach (characterized as a case study) aimed at analyzing the didactic pedagogical potential of this type of methodology in high school. We found that tasks such as those presented and discussed in this paper provide a more significant learning for the students, allowing a better conceptual understanding, becoming still more powerful when one considers the social-cultural context of the students.

Participative site-specific agriculture analysis for smallholders

Site-specific agriculture has been adopted in a high-tech context using, for instance, in situ sensors, satellite images for remote sensing analysis, and some other technological devices. However, farmers and smallholders without the economic resources and required knowledge to use and to access the latest technology seem to find an impediment to precision agricultural practices. This article discusses the possibility of adopting precision agriculture (PA) principles for site-specific management but in a low technology context for such farmers. The proposed methodology to support PA combines low technology dependency and a participatory approach by involving smallholders, farmers and experts. The case studies demonstrate how the interplay of low technology and a participative approach may be suitable for smallholders for site-specific agriculture analysis.

A multicenter, multinational analysis of mitomycin C in refractory metastatic colorectal cancer

Background: A considerable number of metastatic colorectal cancer (mCRC) patients who progress on standard treatment with 5-fluorouracil (5FU), oxaliplatin, irinotecan and monoclonal antibodies, still have adequate performance status and desire further treatment. Mitomycin C (MMC) has been widely used in this context, and despite good tolerability, there are doubts regarding its true benefit. Methods: In order to assess the activity of MMC in the refractory mCRC setting, we retrospectively evaluated 109 heavily pre-treated patients who received MMC as single agent or in combination for mCRC at three different institutions in two countries. Results: Median patient's age was 54 years old, 57% were male and 94% had performance status ECOG 0 or 1. MMC was used in second line in 11%, third line in 38% and fourth line or beyond in 51% of patients. 58% received MMC combinations, mainly with capecitabine. Grade 3 or 4 toxicity was observed in 5% of patients and 6% required dose reductions. Median time to treatment failure (TTF) was 1.7 months with MMC and 3.6 months on the regimen prior to MMC, with a ratio between these TTF below 1 in 82% of patients. Median survival was only 4.5 months (95% confidence interval (CI) of 3.48-5.56). Conclusions: This retrospective data represent the largest reported series of unselected refractory mCRC patients treated with MMC. The median survival of 4.5 months is similar to the survival expected for best supportive care. This lack of activity strongly suggests that MMC should not be routinely used in refractory mCRC. (C) 2012 Elsevier Ltd. All rights reserved.

Association Between Use of Lung-Protective Ventilation With Lower Tidal Volumes and Clinical Outcomes Among Patients Without Acute Respiratory Distress Syndrome A Meta-analysis

Context Lung-protective mechanical ventilation with the use of lower tidal volumes has been found to improve outcomes of patients with acute respiratory distress syndrome (ARDS). It has been suggested that use of lower tidal volumes also benefits patients who do not have ARDS. Objective To determine whether use of lower tidal volumes is associated with improved outcomes of patients receiving ventilation who do not have ARDS. Data Sources MEDLINE, CINAHL, Web of Science, and Cochrane Central Register of Controlled Trials up to August 2012. Study Selection Eligible studies evaluated use of lower vs higher tidal volumes in patients without ARDS at onset of mechanical ventilation and reported lung injury development, overall mortality, pulmonary infection, atelectasis, and biochemical alterations. Data Extraction Three reviewers extracted data on study characteristics, methods, and outcomes. Disagreement was resolved by consensus. Data Synthesis Twenty articles (2822 participants) were included. Meta-analysis using a fixed-effects model showed a decrease in lung injury development (risk ratio [RR], 0.33; 95% CI, 0.23 to 0.47; I-2, 0%; number needed to treat [NNT], 11), and mortality (RR, 0.64; 95% CI, 0.46 to 0.89; I-2, 0%; NNT, 23) in patients receiving ventilation with lower tidal volumes. The results of lung injury development were similar when stratified by the type of study (randomized vs nonrandomized) and were significant only in randomized trials for pulmonary infection and only in nonrandomized trials for mortality. Meta-analysis using a random-effects model showed, in protective ventilation groups, a lower incidence of pulmonary infection (RR, 0.45; 95% CI, 0.22 to 0.92; I-2, 32%; NNT, 26), lower mean (SD) hospital length of stay (6.91 [2.36] vs 8.87 [2.93] days, respectively; standardized mean difference [SMD], 0.51; 95% CI, 0.20 to 0.82; I-2, 75%), higher mean (SD) PaCO2 levels (41.05 [3.79] vs 37.90 [4.19] mm Hg, respectively; SMD, -0.51; 95% CI, -0.70 to -0.32; I-2, 54%), and lower mean (SD) pH values (7.37 [0.03] vs 7.40 [0.04], respectively; SMD, 1.16; 95% CI, 0.31 to 2.02; I-2, 96%) but similar mean (SD) ratios of PaO2 to fraction of inspired oxygen (304.40 [65.7] vs 312.97 [68.13], respectively; SMD, 0.11; 95% CI, -0.06 to 0.27; I-2, 60%). Tidal volume gradients between the 2 groups did not influence significantly the final results. Conclusions Among patients without ARDS, protective ventilation with lower tidal volumes was associated with better clinical outcomes. Some of the limitations of the meta-analysis were the mixed setting of mechanical ventilation (intensive care unit or operating room) and the duration of mechanical ventilation. JAMA. 2012;308(16):1651-1659 www.jama.com

Multidimensional Projections for Visual Analysis of Social Networks

Visual analysis of social networks is usually based on graph drawing algorithms and tools. However, social networks are a special kind of graph in the sense that interpretation of displayed relationships is heavily dependent on context. Context, in its turn, is given by attributes associated with graph elements, such as individual nodes, edges, and groups of edges, as well as by the nature of the connections between individuals. In most systems, attributes of individuals and communities are not taken into consideration during graph layout, except to derive weights for force-based placement strategies. This paper proposes a set of novel tools for displaying and exploring social networks based on attribute and connectivity mappings. These properties are employed to layout nodes on the plane via multidimensional projection techniques. For the attribute mapping, we show that node proximity in the layout corresponds to similarity in attribute, leading to easiness in locating similar groups of nodes. The projection based on connectivity yields an initial placement that forgoes force-based or graph analysis algorithm, reaching a meaningful layout in one pass. When a force algorithm is then applied to this initial mapping, the final layout presents better properties than conventional force-based approaches. Numerical evaluations show a number of advantages of pre-mapping points via projections. User evaluation demonstrates that these tools promote ease of manipulation as well as fast identification of concepts and associations which cannot be easily expressed by conventional graph visualization alone. In order to allow better space usage for complex networks, a graph mapping on the surface of a sphere is also implemented.

Neutron activation analysis for assessing chemical composition of dry dog foods

Brazil holds the second largest population of domestic dogs in the world, with 33 million dogs, only behind the United States. The annual consumption of dog food in the country is 1.75 million tons, corresponding to the World's sixth in trade turnover. Dog food is supposed to be a complete and balanced diet, formulated with high quality ingredients. All nutrients and minerals required for an adequate nutrition of dogs are added to the formulation to ensure longevity and welfare. In this context, the present study aimed at assessing the chemical composition of dry dog foods commercialized in Brazil. Thirty-four samples were acquired in the local market of Piracicaba and analyzed by instrumental neutron activation analysis (INAA) to determine the elements As, Br, Ca, Co, Cr, Cs, Fe, K, La, Na, Rb, Sb, Sc, Se, U, and Zn. In general, the concentrations of Ca, Fe, K, Na, and Zn complied with the values required by the Association of American Feed Control Officials (AAFCO). To evaluate the safety of dog food commercialized in Brazil, further investigation is necessary to better understand the presence of toxic elements found in this study, i.e. Sb and U. INAA was useful for the screening analysis of different types and brands of dry dog foods for the determination of both essential and toxic elements.

Analysis of nonlinear dynamics of vocal folds using high-speed video observation and biomechanical modeling

Primary voice production occurs in the larynx through vibrational movements carried out by vocal folds. However, many problems can affect this complex system resulting in voice disorders. In this context, time-frequency-shape analysis based on embedding phase space plots and nonlinear dynamics methods have been used to evaluate the vocal fold dynamics during phonation. For this purpose, the present work used high-speed video to record the vocal fold movements of three subjects and extract the glottal area time series using an image segmentation algorithm. This signal is used for an optimization method which combines genetic algorithms and a quasi-Newton method to optimize the parameters of a biomechanical model of vocal folds based on lumped elements (masses, springs and dampers). After optimization, this model is capable of simulating the dynamics of recorded vocal folds and their glottal pulse. Bifurcation diagrams and phase space analysis were used to evaluate the behavior of this deterministic system in different circumstances. The results showed that this methodology can be used to extract some physiological parameters of vocal folds and reproduce some complex behaviors of these structures contributing to the scientific and clinical evaluation of voice production. (C) 2010 Elsevier Inc. All rights reserved.

Common bile duct stones: analysis of the videolaparoscopic surgical treatment

CONTEXT: About 9% of the Brazilian population has gallstones and the incidence increases significantly with aging. The choledocholithiasis is found around 15% of these patients, and a third to half of these cases presented as asymptomatic. Once the lithiasis in the common bile duct is characterized through intraoperative cholangiography, the laparoscopic surgical exploration can be done through the transcystic way or directly through choledochotomy. OBJECTIVE: To evaluate the results and outcomes of the laparoscopic treatment of common bile duct lithiasis. METHODS: Seventy consecutive patients were evaluated. They prospectively underwent the treatment of the lithiasis in the common bile duct and the exploration ways were compared according to the following parameters: criteria on their indication, success in the clearance, surgical complications. It was verified that about ½ of the choledocholithiasis carriers did not show any expression of predictive factors (clinical antecedents of jaundice and/or acute pancreatitis, compatible sonographic data and the pertaining lab tests). The laparoscopic exploration through the transcystic way is favored when there are no criteria for the practice of primary choledochotomy, which are: lithiasis in the proximal bile duct, large (over 8 mm) or numerous calculi (multiple calculosis). RESULTS: The transcystic way was employed in about 50% of the casuistic and the choledochotomy in about 30%. A high success rate (around 80%) was achieved in the clearance of the common bile duct stones through laparoscopic exploration. The transcystic way, performed without fluoroscopy or choledochoscopy, attained a low rate of success (around 45%), being 10% of those by transpapilar pushing of calculi less than 3 mm. The exploration through choledochotomy, either primary or secondary, if the latter was performed after the transcystic route failure, showed high success rate (around 95%). When the indication to choledochotomy was primary, the necessity for choledochoscopy through choledochotomy to help in the removal of the calculi was 55%. However, when choledochotomy was performed secondarily, in situations where the common bile duct diameter was larger than 6 mm, the use of choledochoscopy with the same purpose involved about 20% of the cases. There was no mortality in this series. CONCLUSION: The laparoscopic exploration of the common bile duct was related to a low rate of morbidity. Therefore, the use of laparoscopy for the treatment of the lithiasis in the common bile duct depends on the criteria for the choice of the best access, making it a safe procedure with very good results.

A three-pronged approach to social business: a Brazilian multi-case analysis

Social businesses present a new paradigm to capitalism, in which private companies, non-profit organizations and civil society create a new type of business with the main objective of solving social problems with financial sustainability and efficiency through market mechanisms. As any new phenomenon, different authors conceptualize social businesses with distinct views. This article aims to present and characterize three different perspectives of social business definitions: the European, the American and that of the emerging countries. Each one of these views was illustrated by a different Brazilian case. We conclude with the idea that all the cases have similar characteristics, but also relevant differences that are more than merely geographical. The perspectives analyzed in this paper provide an analytical framework for understanding the field of social businesses. Moreover, the cases demonstrate that in the Brazilian context the field of social business is under construction and that as such it draws on different conceptual influences to deal with a complex and challenging reality.

Inclusive business and poverty: prospects in the Brazilian context

Inclusive business is a term currently used to explain the organizations that aim to solve social problems with efficiency and financial sustainability by means of market mechanisms. It can be said that inclusive businesses are those targeted at generating employment and income for groups with little or no market mobility, in keeping with the standards of so-called "decent jobs" and in a self-sustaining manner, i.e., generating profit for the enterprises, and establishing relationships with typical business organizations as suppliers of products and services or in the distribution of this type of production. This article discusses the different concepts found in the scientific literature on inclusive businesses. It also analyses data from a survey conducted with the audiences of Social Corporate Responsibility seminars held by FIEMG. This analysis reveals that prospects, risks and idealizations similar to those found in inclusive business theories can also be found among individuals that run social corporate responsibility projects, even if this designation is new for them. The connection between companies and poverty, especially in relation to inclusive businesses, seems full of stumbling blocks and traps in the Brazilian context.

Evaluation of quality of life in a palliative care context: an integrative literature review

The use of scales that have been validated and standardized for different cultures is very useful for identifying demands in the field of Palliative Care and implementing the most appropriate care. This integrative literature review focuses on instruments assessing the Quality of Life of patients under Palliative Care through a journal search in electronic databases. The study consisted of 49 papers identified in Medline/PubMed, of which 18 met the inclusion criteria previously defined. Information concerning the selected studies is presented and later categorized, with a greater emphasis on the analysis of the psychometric properties of validations of the Palliative Outcome Scale, conducted in three countries. This review enabled the identification of instruments already developed and validated for different cultures, increasing the possibility of knowledge in the field.

Experimental and numerical analysis of dry contact in the pin on disc test

The reduction of friction and wear in systems presenting metal-to-metal contacts, as in several mechanical components, represents a traditional challenge in tribology. In this context, this work presents a computational study based on the linear Archard's wear law and finite element modeling (FEM), in order to analyze unlubricated sliding wear observed in typical pin on disc tests. Such modeling was developed using finite element software Abaqus® with 3-D deformable geometries and elastic–plastic material behavior for the contact surfaces. Archard's wear model was implemented into a FORTRAN user subroutine (UMESHMOTION) in order to describe sliding wear. Modeling of debris and oxide formation mechanisms was taken into account by the use of a global wear coefficient obtained from experimental measurements. Such implementation considers an incremental computation for surface wear based on the nodal displacements by means of adaptive mesh tools that rearrange local nodal positions. In this way, the worn track was obtained and new surface profile is integrated for mass loss assessments. This work also presents experimental pin on disc tests with AISI 4140 pins on rotating AISI H13 discs with normal loads of 10, 35, 70 and 140 N, which represent, respectively, mild, transition and severe wear regimes, at sliding speed of 0.1 m/s. Numerical and experimental results were compared in terms of wear rate and friction coefficient. Furthermore, in the numerical simulation the stress field distribution and changes in the surface profile across the worn track of the disc were analyzed. The applied numerical formulation has shown to be more appropriate to predict mild wear regime than severe regime, especially due to the shorter running-in period observed in lower loads that characterizes this kind of regime.