Using Threads to Overcome Synchronization Delays in Parallel Multiple Progressive Alignment Algorithms

Sao Paulo State Research Foundation-FAPESP

Um piloto de tradução alinhada e anotação em árvore sintática de dependência do grego antigo (AGDT 1.0) pela plataforma Alpheios.net com passagens de Heródoto

This study was developed based on Classical Greek Language classes, reading and translation of texts. There is also the presence of computer elements due to use of Alpheios digital platform. As an example of a larger proposal, this proposal aims at produce translation aligned with the Portuguese and syntactic annotation with the production of the Greek dependency trees. To achieve the goal, we chose Chapter 34, Volume 1 of The Histories from Herodotus. The methods adopted contain a list and description of the instruments and the morphological categories from the guide (manual rules of syntax tree). The procedures adopted are the description of the alignment process and of syntactic annotation. As study results, we have the production line translation and the syntactic annotation of the excerpt 1.34. It was concluded that the study of this text is relevant, because the lexical density of Herodotus it's interesting at future researchers and students that will use the digital platform Alpheios

Sacredness of the constitutional text and interpretive heresy: the brazilian supreme court decision on same-sex unions

The paper provides a close lecture of the arguments and methods of legal construction, employed in the extensive individual opinions written by the Justices of the Brazilian Supreme Court in the case which authorized the same sex civil union. After tracing an outline of the legal problem and his possible solutions, we analyze the individual opinions, showing their methodological syncretism, the use of legal methods and arguments in a contradictory way as well the deficiencies in the reasoning. The Justices use legal arguments, but do not meet the requirements of rationality in the decision-making. We have a rhetorical attempt that aims to satisfy the public opinion than to offer a comprehensive and coherent solution according the normative elements of the Brazilian Federal Constitution of 1988.

Review of The Bible at Qumran: Text, Shape, and Interpretation, edited by Peter W. Flint

Review of The Bible at Qumran: Text, Shape, and Interpretation, edited by Peter W. Flint. Studies in the Dead Sea Scrolls and Related Literature. Grand Rapids, MI: Eerdmans, 2001. Pp. xv + 266. Price: $22.00. ISBN 0-8028-4630-0. This volume is another contribution to the Eerdmans series Studies in the Dead Sea Scrolls and Related Literature. The essays are loosely gathered around the topic "The Bible at Qumran," and the editor has divided the articles into two groups. Part 1, "The Scriptures, the Canon, and the Scrolls," includes articles by J.A. Sanders, B.W. Waltke, E. Ulrich, C.A. Evans, and the editor, P.W. Flint. The contributors to Part 2, "Biblical Interpretation and the Dead Sea Scrolls," are J.C. VanderKam, C.A. Evans, J.E. Bowley, J.M. Scott, M.G. Abegg, and R.W. Wall. Unlike other volumes of collected essays in this series, which have highlighted the work of a single author or published the proceedings of a particular conference, this collection has a more disparate origin. Some contributions were given as papers at the Dead Sea Scrolls Institute of Trinity Western University (Bowley, Ulrich, VanderKam and Wall), one (Waltke) is reprinted from The New International Dictionary of Old Testament Theology and Exegesis (Grand Rapids: Zondervan, 1997), and the rest (Abegg, Evans, Flint, Sanders and Scott) were invited for the volume.

Seeing beyond reading: a survey on visual text analytics

We review recent visualization techniques aimed at supporting tasks that require the analysis of text documents, from approaches targeted at visually summarizing the relevant content of a single document to those aimed at assisting exploratory investigation of whole collections of documents.Techniques are organized considering their target input materialeither single texts or collections of textsand their focus, which may be at displaying content, emphasizing relevant relationships, highlighting the temporal evolution of a document or collection, or helping users to handle results from a query posed to a search engine.We describe the approaches adopted by distinct techniques and briefly review the strategies they employ to obtain meaningful text models, discuss how they extract the information required to produce representative visualizations, the tasks they intend to support and the interaction issues involved, and strengths and limitations. Finally, we show a summary of techniques, highlighting their goals and distinguishing characteristics. We also briefly discuss some open problems and research directions in the fields of visual text mining and text analytics.

A hymenopterists' guide to the Hymenoptera Anatomy Ontology: utility, clarification, and future directions

Hymenoptera exhibit an incredible diversity of phenotypes, the result of similar to 240 million years of evolution and the primary subject of more than 250 years of research. Here we describe the history, development, and utility of the Hymenoptera Anatomy Ontology (HAO) and its associated applications. These resources are designed to facilitate accessible and extensible research on hymenopteran phenotypes. Outreach with the hymenopterist community is of utmost importance to the HAO project, and this paper is a direct response to questions that arose from project workshops. In a concerted attempt to surmount barriers of understanding, especially regarding the format, utility, and development of the HAO, we discuss the roles of homology, "preferred terms", and "structural equivalency". We also outline the use of Universal Resource Identifiers (URIs) and posit that they are a key element necessary for increasing the objectivity and repeatability of science that references hymenopteran anatomy. Pragmatically, we detail a mechanism (the "URI table") by which authors can use URIs to link their published text to the HAO, and we describe an associated tool (the "Analyzer") to derive these tables. These tools, and others, are available through the HAO Portal website (http://portal.hymao.org). We conclude by discussing the future of the HAO with respect to digital publication, cross-taxon ontology alignment, the advent of semantic phenotypes, and community-based curation.

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.

Rescue technique for salvaging toric intraocular lens alignment

Accurate alignment of a toric intraocular lens (IOL) is a requisite to achieving the intended reduction in astigmatism at the time of cataract surgery. However, it requires a reasonably clear view of the limbal vascular anatomy, which is sometimes altered by chemosis from a subconjunctival anesthetic injection or a hemorrhage. We describe a technique that can quickly restore vascular anatomy and facilitate toric IOL alignment.

Mini-Mental State Examination sentence writing among community-dwelling elderly adults in Brazil: text fluency and grammar complexity

Background: In normal aging, the decrease in the syntactic complexity of written production is usually associated with cognitive deficits. This study was aimed to analyze the quality of older adults' textual production indicated by verbal fluency (number of words) and grammatical complexity (number of ideas) in relation to gender, age, schooling, and cognitive status. Methods: From a probabilistic sample of community-dwelling people aged 65 years and above (n = 900), 577 were selected on basis of their responses to the Mini-Mental State Examination (MMSE) sentence writing, which were submitted to content analysis; 323 were excluded as they left the item blank or performed illegible or not meaningful responses. Education adjusted cut-off scores for the MMSE were used to classify the participants as cognitively impaired or unimpaired. Total and subdomain MMSE scores were computed. Results: 40.56% of participants whose answers to the MMSE sentence were excluded from the analyses had cognitive impairment compared to 13.86% among those whose answers were included. The excluded participants were older and less educated. Women and those older than 80 years had the lowest scores in the MMSE. There was no statistically significant relationship between gender, age, schooling, and textual performance. There was a modest but significant correlation between number of words written and the scores in the Language subdomain. Conclusions: Results suggest the strong influence of schooling and age over MMSE sentence performance. Failing to write a sentence may suggest cognitive impairment, yet, instructions for the MMSE sentence, i.e. to produce a simple sentence, may limit its clinical interpretation.

Preimplantation development regulatory pathway construction through a text-mining approach

Background: The integration of sequencing and gene interaction data and subsequent generation of pathways and networks contained in databases such as KEGG Pathway is essential for the comprehension of complex biological processes. We noticed the absence of a chart or pathway describing the well-studied preimplantation development stages; furthermore, not all genes involved in the process have entries in KEGG Orthology, important information for knowledge application with relation to other organisms. Results: In this work we sought to develop the regulatory pathway for the preimplantation development stage using text-mining tools such as Medline Ranker and PESCADOR to reveal biointeractions among the genes involved in this process. The genes present in the resulting pathway were also used as seeds for software developed by our group called SeedServer to create clusters of homologous genes. These homologues allowed the determination of the last common ancestor for each gene and revealed that the preimplantation development pathway consists of a conserved ancient core of genes with the addition of modern elements. Conclusions: The generation of regulatory pathways through text-mining tools allows the integration of data generated by several studies for a more complete visualization of complex biological processes. Using the genes in this pathway as “seeds” for the generation of clusters of homologues, the pathway can be visualized for other organisms. The clustering of homologous genes together with determination of the ancestry leads to a better understanding of the evolution of such process.

Clinical rearfoot and knee static alignment measurements are not associated with patellofemoral pain syndrome

The aim of the present study was to investigate the association between the patellofemoral pain syndrome and the clinical static measurements: the rearfoot and the Q angles. The design was a cross-sectional, observational, case-control study. We evaluated 77 adults (both genders), 30 participants with patellofemoral pain syndrome, and 47 controls. We measured the rearfoot and Q angles by photogrammetry. Independent t-tests were used to compare outcome continuous measures between groups. Outcome continuous data were also transformed into categorical clinical classifications, in order to verify their statistical association with the dysfunction, and χ2 tests for multiple responses were used. There were no differences between groups for rearfoot angle [mean differences: 0.2º (95%CI -1.4-1.8)] and Q angle [mean differences: -0.3º (95%CI -3.0-2.4). No associations were found between increased rearfoot valgus [Odds Ratio: 1.29 (95%CI 0.51-3.25)], as well as increased Q angle [Odds Ratio: 0.77 (95%CI 0.31-1.93)] and the patellofemoral pain syndrome occurrence. Although widely used in clinical practice and theoretically thought, it cannot be affirmed that increased rearfoot valgus and increased Q angle, when statically measured in relaxed stance, are associated with patellofemoral pain syndrome (PFPS). These measures may have limited applicability in screening of the PFPS development.

Quantification of cellular action fibers alignment from confocal microscopic images.

The cellular rheology has recently undergone a rapid development with particular attention to the cytoskeleton mechanical properties and its main components - actin filaments, intermediate filaments, microtubules and crosslinked proteins. However it is not clear what are the cellular structural changes that directly affect the cell mechanical properties. Thus, in this work, we aimed to quantify the structural rearrangement of these fibers that may emerge in changes in the cell mechanics. We created an image analysis platform to study smooth muscle cells from different arteries: aorta, mammary, renal, carotid and coronary and processed respectively 31, 29, 31, 30 and 35 cell image obtained by confocal microscopy. The platform was developed in Matlab (MathWorks) and it uses the Sobel operator to determine the actin fiber image orientation of the cell, labeled with phalloidin. The Sobel operator is used as a filter capable of calculating the pixel brightness gradient, point to point, in the image. The operator uses vertical and horizontal convolution kernels to calculate the magnitude and the angle of the pixel intensity gradient. The image analysis followed the sequence: (1) opens a given cells image set to be processed; (2) sets a fix threshold to eliminate noise, based on Otsu's method; (3) detect the fiber edges in the image using the Sobel operator; and (4) quantify the actin fiber orientation. Our first result is the probability distribution II(Δθ) to find a given fiber angle deviation (Δθ) from the main cell fiber orientation θ0. The II(Δθ) follows an exponential decay II(Δθ) = Aexp(-αΔθ) regarding to its θ0. We defined and determined a misalignment index α of the fibers of each artery kind: coronary αCo = (1.72 ‘+ or =’ 0.36)rad POT -1; renal αRe = (1.43 + or - 0.64)rad POT -1; aorta αAo = (1.42 + or - 0.43)rad POT -1; mammary αMa = (1.12 + or - 0.50)rad POT -1; and carotid αCa = (1.01 + or - 0.39)rad POT -1. The α of coronary and carotid are statistically different (p < 0.05) among all analyzed cells. We discussed our results correlating the misalignment index data with the experimental cell mechanical properties obtained by using Optical Magnetic Twisting Cytometry with the same group of cells.

Learning Democracy Together in School? : Student and Teacher Attitudes in Bosnia and Herzegovina

The principal aim of this study is to examine attitudes and values, through questionnaires, among students and teachers in the last grade of primary school (grade 8) regarding issues related to authoritarianism, democracy, human rights, children rights, conflict resolution and legislation in Bosnia and Herzegovina. A second aim is to explore and analyze the role of the international community in the democratization and education processes in the light of globalization in this country through secondary sources of data, site visits and observations. Analysis of the student sample reveals suspicion towards democracy, especially when democracy was associated with politics and politicians. When the issue of democracy was de-contextualized from Bosnia and Herzegovina realities in the questionnaire, students showed more positive attitudes towards it. Students generally agreed with very strong authoritarian statements. High achieving students were more democratic, more socially responsible, more tolerant regarding attitudes towards religion, race and disabilities, and less authoritarian compared to low achievers. High achievers felt that they had influence over daily events, and were positive towards social and civil engagement. High achievers viewed politics negatively, but had high scores on the democracy scale. High achievers also agreed to a larger extent that it is acceptable to break the law. The more authoritarian students were somewhat more prone to respond that it is not acceptable to break the law. The major findings from the teacher sample show that teachers who agreed with non-peaceful mediation, and had a non-forgiving and rigid approach to interpersonal conflicts, also agreed with strong authoritarian statements and were less democratic. In general, teachers valued students who behave respectfully, have a good upbringing and are obedient. They were very concerned about the general status of education in society, which they felt was becoming marginalized. Teachers were not happy with the overloaded curricula and they showed an interest in more knowledge and skills to help children with traumatic war experiences. When asked about positive reforms, teachers were highly critical of, and dissatisfied with, the educational situation. Bosnia and Herzegovina is undergoing a transition from a state-planned economy and one party system to a market economy and a multi party system. During this transition, the country has become more involved in the globalization process than ever. Today the country is a semi-protectorate where international authorities intervene when necessary. The International community is attempting to introduce western democracy and some of the many complexities in this process are discussed in this study. Globalization processes imply contradictory demands and pressures on the education system. On one hand, economic liberalization has affected education policies —a closer alignment between education and economic competitiveness. On the other hand, there is a political and ideological globalization process underlying the importance of human rights, and the inclusiveness of education for all children. Students and teachers are caught between two opposing ideals — competition and cooperation.

Variance Reduction in Analytical Chemistry : New Numerical Methods in Chemometrics and Molecular Simulation

This thesis is based on five papers addressing variance reduction in different ways. The papers have in common that they all present new numerical methods. Paper I investigates quantitative structure-retention relationships from an image processing perspective, using an artificial neural network to preprocess three-dimensional structural descriptions of the studied steroid molecules. Paper II presents a new method for computing free energies. Free energy is the quantity that determines chemical equilibria and partition coefficients. The proposed method may be used for estimating, e.g., chromatographic retention without performing experiments. Two papers (III and IV) deal with correcting deviations from bilinearity by so-called peak alignment. Bilinearity is a theoretical assumption about the distribution of instrumental data that is often violated by measured data. Deviations from bilinearity lead to increased variance, both in the data and in inferences from the data, unless invariance to the deviations is built into the model, e.g., by the use of the method proposed in paper III and extended in paper IV. Paper V addresses a generic problem in classification; namely, how to measure the goodness of different data representations, so that the best classifier may be constructed. Variance reduction is one of the pillars on which analytical chemistry rests. This thesis considers two aspects on variance reduction: before and after experiments are performed. Before experimenting, theoretical predictions of experimental outcomes may be used to direct which experiments to perform, and how to perform them (papers I and II). After experiments are performed, the variance of inferences from the measured data are affected by the method of data analysis (papers III-V).