AllerTOP - a server for in silico prediction of allergens

Background: Allergy is a form of hypersensitivity to normally innocuous substances, such as dust, pollen, foods or drugs. Allergens are small antigens that commonly provoke an IgE antibody response. There are two types of bioinformatics-based allergen prediction. The first approach follows FAO/WHO Codex alimentarius guidelines and searches for sequence similarity. The second approach is based on identifying conserved allergenicity-related linear motifs. Both approaches assume that allergenicity is a linearly coded property. In the present study, we applied ACC pre-processing to sets of known allergens, developing alignment-independent models for allergen recognition based on the main chemical properties of amino acid sequences.Results: A set of 684 food, 1,156 inhalant and 555 toxin allergens was collected from several databases. A set of non-allergens from the same species were selected to mirror the allergen set. The amino acids in the protein sequences were described by three z-descriptors (z1, z2 and z3) and by auto- and cross-covariance (ACC) transformation were converted into uniform vectors. Each protein was presented as a vector of 45 variables. Five machine learning methods for classification were applied in the study to derive models for allergen prediction. The methods were: discriminant analysis by partial least squares (DA-PLS), logistic regression (LR), decision tree (DT), naïve Bayes (NB) and k nearest neighbours (kNN). The best performing model was derived by kNN at k = 3. It was optimized, cross-validated and implemented in a server named AllerTOP, freely accessible at http://www.pharmfac.net/allertop. AllerTOP also predicts the most probable route of exposure. In comparison to other servers for allergen prediction, AllerTOP outperforms them with 94% sensitivity.Conclusions: AllerTOP is the first alignment-free server for in silico prediction of allergens based on the main physicochemical properties of proteins. Significantly, as well allergenicity AllerTOP is able to predict the route of allergen exposure: food, inhalant or toxin. © 2013 Dimitrov et al.; licensee BioMed Central Ltd.

Assessment of social cognition in bipolar disorder

Background: Impairment in social cognition may contribute to deficits in social functioning in patients with bipolar disorder (BD). In this study, a complex social cognition task was administered during a neuroimaging session. The behavioral and neural correlates of social cogniton in patients with BD were compared to healthy comparison (HC) subjects. Methods: The task was administered to 25 HC and 25 patients with depression scores ranging from euthymic to depressed at the time of assessment. The task required participants to evaluate situations that were “enhancing” or “threatening” to self-esteem, directed at both oneself, and at other people. For instance, self-esteem enhancing scenarios involved vignettes of activities such as receiving praise during a sports game, while a threatening scenario involved, for example, receiving criticism at a party. Participants were then required to evaluate characters in the scenarios on the basis of positive (“kind”) or negative (“mean”) descriptors. Evaluations were classified from extremely negative to extremely positive. The frequencies of behavioral responses were analyzed using chi-square tests and fMRI data were analyzed using Statistical Parametric Mapping software. Results: Patients differed significantly from HCs in their evaluation of threatening scenarios, directed at both oneself and at other people (p<0.001). Patients had a lower proportion of responses in the neutral category, and more responses in the positive and negative categories, relative to HCs. Neuroimaging results reveal differential patterns of prefrontal-cortical and limbic-subcortical activation in BDs throughout the task [p<0.05 (unc.)]. Conclusions: Findings will contribute to understanding difficulty in interpersonal functioning in patients with BD.

Quantitative analysis of solid-state processes studied with isothermal microcalorimetry

Quantitative analysis of solid-state processes from isothermal microcalorimetric data is straightforward if data for the total process have been recorded and problematic (in the more likely case) when they have not. Data are usually plotted as a function of fraction reacted (α); for calorimetric data, this requires knowledge of the total heat change (Q) upon completion of the process. Determination of Q is difficult in cases where the process is fast (initial data missing) or slow (final data missing). Here we introduce several mathematical methods that allow the direct calculation of Q by selection of data points when only partial data are present, based on analysis with the Pérez-Maqueda model. All methods in addition allow direct determination of the reaction mechanism descriptors m and n and from this the rate constant, k. The validity of the methods is tested with the use of simulated calorimetric data, and we introduce a graphical method for generating solid-state power-time data. The methods are then applied to the crystallization of indomethacin from a glass. All methods correctly recovered the total reaction enthalpy (16.6 J) and suggested that the crystallization followed an Avrami model. The rate constants for crystallization were determined to be 3.98 × 10-6, 4.13 × 10-6, and 3.98 × 10 -6 s-1 with methods 1, 2, and 3, respectively. © 2010 American Chemical Society.

The dynamics of movement: Toward a definition of a Latin American identity in contemporary fiction

Concha Meléndez opened up a venue for the discussion of a Latin American identity in works of literature when she implied that the great Latin American novel would gestate in the cities, the space where the typical Latin American would achieve an ideal state of consciousness and intellectual capabilities. ^ Her point of view mirrored nineteenth-century debate on a Latin American identity. Similar to her viewpoint, intellectuals of this period viewed the cities and their inhabitants of European extraction, as the ideal spaces and people on which an identity could be defined. However, the present state of urban and rural areas in Latin America demonstrates that there is no such clear-cut division of city and countryside or of their inhabitants. The dynamics of movement, from rural to urban areas, of people of diverse ethnic, and socioeconomic backgrounds, make it difficult to uphold descriptors of space, race, or culture, as sole descriptors of an identity. ^ A study of five twentieth-century novels from North and South America, La muerte de Artemio Cruz (1962), Hasta no verte Jesús mío (1969), Los ríos profundos (1981), La casa de los espíritus (1982), and Los años con Laura Díaz (1999) reveal that the dynamism of movement, between countryside, and cities of peoples of distinct races and social backgrounds, hamper the definition of a collective identity in specific spaces. As characters move, they are constantly reconfiguring their identities and creating tensions and conflicts that intensify social, racial and economic divisions in society. This makes it difficult to ascribe permanent identity descriptors, much less define a collective identity. ^ However, as writers of fiction address the malaise in Latin American societies, they have unearthed descriptors such as history, economy, land, and movement that advance a collective definition of self in these societies. Additionally, female characters have been granted a new identity. The overwhelming evidence in this study points to ‘land’ as the prime factor in the identity dilemma and suggests that a definition will not be possible until the vast landless populace is granted a space they can call home. Only then, perhaps, will Meléndez novel surface. ^

Knowledge assisted data management and retrieval in multimedia database systems

With the proliferation of multimedia data and ever-growing requests for multimedia applications, there is an increasing need for efficient and effective indexing, storage and retrieval of multimedia data, such as graphics, images, animation, video, audio and text. Due to the special characteristics of the multimedia data, the Multimedia Database management Systems (MMDBMSs) have emerged and attracted great research attention in recent years. Though much research effort has been devoted to this area, it is still far from maturity and there exist many open issues. In this dissertation, with the focus of addressing three of the essential challenges in developing the MMDBMS, namely, semantic gap, perception subjectivity and data organization, a systematic and integrated framework is proposed with video database and image database serving as the testbed. In particular, the framework addresses these challenges separately yet coherently from three main aspects of a MMDBMS: multimedia data representation, indexing and retrieval. In terms of multimedia data representation, the key to address the semantic gap issue is to intelligently and automatically model the mid-level representation and/or semi-semantic descriptors besides the extraction of the low-level media features. The data organization challenge is mainly addressed by the aspect of media indexing where various levels of indexing are required to support the diverse query requirements. In particular, the focus of this study is to facilitate the high-level video indexing by proposing a multimodal event mining framework associated with temporal knowledge discovery approaches. With respect to the perception subjectivity issue, advanced techniques are proposed to support users' interaction and to effectively model users' perception from the feedback at both the image-level and object-level.

Climatic Controls on Phytoplankton Biomass in a Sub-tropical Estuary, Florida Bay, USA

The extraction of climatic signals from time series of biogeochemical data is further complicated in estuarine regions because of the dynamic interaction of land, ocean, and atmosphere. We explored the behavior of potential global and regional climatic stressors to isolate specific shifts or trends, which could have a forcing role on the behavior of biogeochemical descriptors of water quality and phytoplankton biomass from Florida Bay, as an example of a sub-tropical estuary. We performed statistical analysis and subdivided the bay into six zones having unique biogeochemical characteristics. Significant shifts in the drivers were identified in all the chlorophyll a time series. Chlorophyll a concentrations closely follow global forcing and display a generalized declining trend on which seasonal oscillations are superimposed, and it is only interrupted by events of sudden increase triggered by storms which are followed by a relatively rapid return to pre-event conditions trailing again the long-term trend.

Periphyton light transmission relationships in Florida Bay and the Florida Keys, USA

Light transmission was measured through intact, submerged periphyton communities on artificial seagrass leaves. The periphyton communities were representative of the communities on Thalassia testudinum in subtropical seagrass meadows. The periphyton communities sampled were adhered carbonate sediment, coralline algae, and mixed algal assemblages. Crustose or film-forming periphyton assemblages were best prepared for light transmission measurements using artificial leaves fouled on both sides, while measurements through three-dimensional filamentous algae required the periphyton to be removed from one side. For one-sided samples, light transmission could be measured as the difference between fouled and reference artificial leaf samples. For two-sided samples, the percent periphyton light transmission to the leaf surface was calculated as the square root of the fraction of incident light. Linear, exponential, and hyperbolic equations were evaluated as descriptors of the periphyton dry weight versus light transmission relationship. Hyperbolic and exponential decay models were superior to linear models and exhibited the best fits for the observed relationships. Differences between the coefficients of determination (r2) of hyperbolic and exponential decay models were statistically insignificant. Constraining these models for 100% light transmission at zero periphyton load did not result in any statistically significant loss in the explanatory capability of the models. In most all cases, increasing model complexity using three-parameter models rather than two-parameter models did not significantly increase the amount of variation explained. Constrained two-parameter hyperbolic or exponential decay models were judged best for describing the periphyton dry weight versus light transmission relationship. On T. testudinum in Florida Bay and the Florida Keys, significant differences were not observed in the light transmission characteristics of the varying periphyton communities at different study sites. Using pooled data from the study sites, the hyperbolic decay coefficient for periphyton light transmission was estimated to be 4.36 mg dry wt. cm−2. For exponential models, the exponential decay coefficient was estimated to be 0.16 cm2 mg dry wt.−1.

Covalent protein adduction by drugs of abuse

Recreational abuse of the drugs cocaine, methamphetamine, and morphine continues to be prevalent in the United States of America and around the world. While numerous methods of detection exist for each drug, they are generally limited by the lifetime of the parent drug and its metabolites in the body. However, the covalent modification of endogenous proteins by these drugs of abuse may act as biomarkers of exposure and allow for extension of detection windows for these drugs beyond the lifetime of parent molecules or metabolites in the free fraction. Additionally, existence of covalently bound molecules arising from drug ingestion can offer insight into downstream toxicities associated with each of these drugs. This research investigated the metabolism of cocaine, methamphetamine, and morphine in common in vitro assay systems, specifically focusing on the generation of reactive intermediates and metabolites that have the potential to form covalent protein adducts. Results demonstrated the formation of covalent adduction products between biological cysteine thiols and reactive moieties on cocaine and morphine metabolites. Rigorous mass spectrometric analysis in conjunction with in vitro metabolic activation, pharmacogenetic reaction phenotyping, and computational modeling were utilized to characterize structures and mechanisms of formation for each resultant thiol adduction product. For cocaine, data collected demonstrated the formation of adduction products from a reactive arene epoxide intermediate, designating a novel metabolic pathway for cocaine. In the case of morphine, data expanded on known adduct-forming pathways using sensitive and selective analysis techniques, following the known reactive metabolite, morphinone, and a proposed novel metabolite, morphine quinone methide. Data collected in this study describe novel metabolic events for multiple important drugs of abuse, culminating in detection methods and mechanistic descriptors useful to both medical and forensic investigators when examining the toxicology associated with cocaine, methamphetamine, and morphine.

A meta -analysis of empirical research studies on resilience among students at -risk for school failure

Being at-risk is a growing problem in the U.S. because of disturbing societal trends such as unemployment, divorce, substance abuse, child abuse and neglect, and the new threat of terrorist violence. Resilience characterizes individuals who rebound from or adapt to adversities such as these, and academic resilience distinguishes at-risk students who succeed in school despite hardships. ^ The purpose of this research was to perform a meta-analysis to examine the power of resilience and to suggest ways educators might improve academic resilience, which was operationalized by satisfactory test scores and grades. In order to find all studies that were relevant to academic resilience in at-risk kindergarten through 12th-grade students, extensive electronic and hardcopy searches were conducted, and these resulted in a database of 421 articles. Two hundred eighty seven of these were rejected quickly, because they were not empirical research. Upon further examination, another 106 were rejected for not meeting study protocol criteria. Ultimately, 28 studies were coded for study level descriptors and effect size variables. ^ Protective factors for resilience were found to originate in physical, psychological, and behavioral domains on proximal/intraindividual, transitional/intrafamilial, or distal/extrafamilial levels. Effect sizes (ESs) for these were weighted and the means for each level or category were interpreted by commonly accepted benchmarks. Mean effect sizes for proximal (M = .27) and for transitional (M = .15) were small but significant. The mean effect size for the distal level was insignificant. This supported the hypotheses that the proximal level was the source of most protective factors for academic resilience in at-risk students followed by the transitional level. The distal effect size warranted further research particularly in light of the small number of studies (n = 11) contributing effect sizes to that category. A homogeneity test indicated a search for moderators, i.e., study variables affecting outcomes, was justified. “Category” was the largest moderator. Graphs of weighted mean effect sizes in the physical, psychological, and behavioral domains were plotted for each level to better illustrate the findings of the meta-analysis. Suggestions were made for combining resilience development with aspects of positive psychology to promote resilience in the schools. ^

Development, validation and uncertainty analysis of quantitative structure and activity relationship models for Log P of disinfection by -products

Hydrophobicity as measured by Log P is an important molecular property related to toxicity and carcinogenicity. With increasing public health concerns for the effects of Disinfection By-Products (DBPs), there are considerable benefits in developing Quantitative Structure and Activity Relationship (QSAR) models capable of accurately predicting Log P. In this research, Log P values of 173 DBP compounds in 6 functional classes were used to develop QSAR models, by applying 3 molecular descriptors, namely, Energy of the Lowest Unoccupied Molecular Orbital (ELUMO), Number of Chlorine (NCl) and Number of Carbon (NC) by Multiple Linear Regression (MLR) analysis. The QSAR models developed were validated based on the Organization for Economic Co-operation and Development (OECD) principles. The model Applicability Domain (AD) and mechanistic interpretation were explored. Considering the very complex nature of DBPs, the established QSAR models performed very well with respect to goodness-of-fit, robustness and predictability. The predicted values of Log P of DBPs by the QSAR models were found to be significant with a correlation coefficient R2 from 81% to 98%. The Leverage Approach by Williams Plot was applied to detect and remove outliers, consequently increasing R 2 by approximately 2% to 13% for different DBP classes. The developed QSAR models were statistically validated for their predictive power by the Leave-One-Out (LOO) and Leave-Many-Out (LMO) cross validation methods. Finally, Monte Carlo simulation was used to assess the variations and inherent uncertainties in the QSAR models of Log P and determine the most influential parameters in connection with Log P prediction. The developed QSAR models in this dissertation will have a broad applicability domain because the research data set covered six out of eight common DBP classes, including halogenated alkane, halogenated alkene, halogenated aromatic, halogenated aldehyde, halogenated ketone, and halogenated carboxylic acid, which have been brought to the attention of regulatory agencies in recent years. Furthermore, the QSAR models are suitable to be used for prediction of similar DBP compounds within the same applicability domain. The selection and integration of various methodologies developed in this research may also benefit future research in similar fields.

Produção do mestrado profissional em ensino de ciências naturais e matemática da UFRN (física e química/2005-2012): papel dos documentos oficiais e características dos produtos educacionais

The importance of the Professionals Master in the field of science education is revealed by the recognition that they provide, to practicing teachers, in particular, training spaces for reflection and application of knowledge. This work appears in the context of the project "Research and training in teaching science and mathematics: a cutout of academic production in the northeast and overview of formative action in basic education" on the Centre for Education program, which main objective was to conduct studies description, analysis and evaluation of the academic production of Postgraduate Programs in Science Teaching of UFRPE, UFRN and UEPB and investigate the contribution of continuing education in stricto sensu level, of graduated teachers to improve the quality of basic education . We sought to examine a cut of academic production PPGECNM / UFRN, taking as reference dissertations of Natural Sciences, finished between the years 2005 and 2012, which have developed and applied educational products for high school students. More specifically we sought to conduct a general characterization of the dissertations analyzed for basic descriptors, to understand if and how the official documents governing the Brazilian education, especially science education, subsidized development of dissertations and identify current trends for science teaching are addressed and which ones are used in preparing the product of dissertations. The survey was based on documentary analysis, a type of qualitative approach in which the documents are objects of study in themselves. The results revealed that most of the work was developed in public schools, on subjects of physics and chemistry. During analytical reading of the text of the dissertations was observed that, in its construction, most of them addressed somehow, official documents governing the Brazilian educational system, that the products are basically teaching units and teaching approaches that are more focused on Experimentation and History and Philosophy of Science

Análise de conceito do diagnóstico de enfermagem autocontrole ineficaz da saúde em pacientes submetidos à hemodiálise

The concept analysis process carefully examines the description and uses of a word or term, enabling the standardization of language, in addition to providing representation to the profession, and facilitate the work of taxonomies. The aim of the study was to analyze the concept of nursing diagnosis ineffective self-health in patients undergoing hemodialysis. Study concept analysis, based on Walker and Avant model and operationalized through integrative literature review. The databases searched were: SCOPUS, CINAHL, PUBMED, LILACS and COCHRANE, with descriptors: Selfmanagement, Adherence and Hemodialysis. The inclusion criteria were: articles published in the last five years, complete articles are available free in selected databases; articles available in Portuguese, English or Spanish; and articles that address the self-concept of health, the antecedents and the consequent. And Exclusion: editorials, letters to the editor, theses and dissertations. The survey of the articles occurred in the months from January to March 2014. The initial sample of 16785 articles, with 11748 in PUBMED, 4767 in Scopus, 174 in CINAHL, the Cochrane 70 and 26 in LILACS. After applying the criteria, 76 articles were selected, 19 in CINAHL, 18 in PUBMED, 30 in Scopus, and 9 in LILACS. In analyzing the data, given that the concept was sought in the literature was self-health, was held interpretation to ineffective self-health diagnosis through the transposition in the denial of the attributes, antecedents and consequences identified. It is noteworthy that the terms identified in the literature as defining characteristics and related factors of the diagnosis under study were added to the survey, not even the transposition into opposite term is possible. The results show that the concept developed for the inefficient self-health diagnosis was: the patient's inability to control habits and achieve the negotiated with professionals therapeutic targets, resulting in health complications. 33 antecedents relating to social, psychological and therapeutic aspects and 16 consequential, involving physiological, social, psychological and therapeutic aspects were identified. Thus, it is concluded that the ineffective self-health concept is broad and involves individual patient factors and the therapeutic relationship between patient and professionals. It is believed that the study contributed to the improvement of diagnosis in renal clientele, besides being an important base for the growth of the scientific body of nursing, subsidizing the development of own technology area

Técnica para segmentação automática de imagens microscópicas de componentes sanguíneos e classificação diferencial de leucócitos baseada em lógica fuzzy

Automatic detection of blood components is an important topic in the field of hematology. The segmentation is an important stage because it allows components to be grouped into common areas and processed separately and leukocyte differential classification enables them to be analyzed separately. With the auto-segmentation and differential classification, this work is contributing to the analysis process of blood components by providing tools that reduce the manual labor and increasing its accuracy and efficiency. Using techniques of digital image processing associated with a generic and automatic fuzzy approach, this work proposes two Fuzzy Inference Systems, defined as I and II, for autosegmentation of blood components and leukocyte differential classification, respectively, in microscopic images smears. Using the Fuzzy Inference System I, the proposed technique performs the segmentation of the image in four regions: the leukocyte’s nucleus and cytoplasm, erythrocyte and plasma area and using the Fuzzy Inference System II and the segmented leukocyte (nucleus and cytoplasm) classify them differentially in five types: basophils, eosinophils, lymphocytes, monocytes and neutrophils. Were used for testing 530 images containing microscopic samples of blood smears with different methods. The images were processed and its accuracy indices and Gold Standards were calculated and compared with the manual results and other results found at literature for the same problems. Regarding segmentation, a technique developed showed percentages of accuracy of 97.31% for leukocytes, 95.39% to erythrocytes and 95.06% for blood plasma. As for the differential classification, the percentage varied between 92.98% and 98.39% for the different leukocyte types. In addition to promoting auto-segmentation and differential classification, the proposed technique also contributes to the definition of new descriptors and the construction of an image database using various processes hematological staining

Segmentação fuzzy de objetos tridimensionais com propriedades texturais

Digital image segmentation is the process of assigning distinct labels to different objects in a digital image, and the fuzzy segmentation algorithm has been used successfully in the segmentation of images from several modalities. However, the traditional fuzzy segmentation algorithm fails to segment objects that are characterized by textures whose patterns cannot be successfully described by simple statistics computed over a very restricted area. In this paper we present an extension of the fuzzy segmentation algorithm that achieves the segmentation of textures by employing adaptive affinity functions as long as we extend the algorithm to tridimensional images. The adaptive affinity functions change the size of the area where they compute the texture descriptors, according to the characteristics of the texture being processed, while three dimensional images can be described as a finite set of two-dimensional images. The algorithm then segments the volume image with an appropriate calculation area for each texture, making it possible to produce good estimates of actual volumes of the target structures of the segmentation process. We will perform experiments with synthetic and real data in applications such as segmentation of medical imaging obtained from magnetic rosonance

A formação do nutricionista para atuação no SUS: um olhar sobre a produção científica obrigatória dos cursos do Rio Grande do Norte

The National Curricular Guidelines for nutrition course predict training directed to the work in the Unified Health System (SUS) and the mandatory completion of course work. The aim of this study was to analyze the formation of dieticians in Rio Grande do Norte state/Brazil to work in the SUS, from the compulsory scientific production provided for training. This is a bibliometric study, quantitative approach, performed with completion of course works of five nutrition undergraduate courses in Rio Grande do Norte state in the years 2013/2013. From the reading of the works, the following variables were collected: nature of the institution, institution administrative category, location, work title, number of authors, work format, titration of the teacher advisor, study type, area of interest, scenery of accomplishment, submission to the ethics committee, suitability of descriptors and, as pertaining to the field of public health, the subfield of public health and the theme. The pedagogical projects of the courses were read and were identified opportunities to develop research in the graduation. For detection of significant categories we applied the Pearson chisquare test. We analyzed 195 works, coming mostly belonging to universities courses (79.0%) and private institutions (56.4%). A higher frequency of articles (68.2%), developed by one student (65.6%), guided by master teachers (57.9%), with cross-sectional study design (49.2%), conducted in laboratory (25%) and without submission to the ethics committee in research (49.2%) was find. The median adequacy of descriptors was 50%. As for the interest of the study, there was a higher frequency of work in the field of public health (p <0.001), within this subfield highlighting the nutritional epidemiology (63.0%) (p <0.001) and the subject nutrition assessment (57, 4%) (p <0.001). In cut on three major areas of dietician performance, was significant performing work in the field of public health in public institutions (p <0.05). The presence of complementary activities was unanimous in the pedagogical projects of the courses. The results of the study showed some methodological weaknesses in the research approaches, as well as a hegemonic positivist training. Despite the emphasis on public health, it was noticed little approximation of policies and nutrition programs in the context of the mandatory recearch of Rio Grande do Norte state nutrition courses.