Inferring genome trees by using a filter to eliminate phylogenetically discordant sequences and a distance matrix based on mean normalized BLASTP scores

Darwin's paradigm holds that the diversity of present-day organisms has arisen via a process of genetic descent with modification, as on a bifurcating tree. Evidence is accumulating that genes are sometimes transferred not along lineages but rather across lineages. To the extent that this is so, Darwin's paradigm can apply only imperfectly to genomes, potentially complicating or perhaps undermining attempts to reconstruct historical relationships among genomes (i.e., a genome tree). Whether most genes in a genome have arisen via treelike (vertical) descent or by lateral transfer across lineages can be tested if enough complete genome sequences are used. We define a phylogenetically discordant sequence (PDS) as an open reading frame (ORF) that exhibits patterns of similarity relationships statistically distinguishable from those of most other ORFs in the same genome. PDSs represent between 6.0 and 16.8% (mean, 10.8%) of the analyzable ORFs in the genomes of 28 bacteria, eight archaea, and one eukaryote (Saccharomyces cerevisiae). In this study we developed and assessed a distance-based approach, based on mean pairwise sequence similarity, for generating genome trees. Exclusion of PDSs improved bootstrap support for basal nodes but altered few topological features, indicating that there is little systematic bias among PDSs. Many but not all features of the genome tree from which PDSs were excluded are consistent with the 16S rRNA tree.

Tele-education and competencies assessment to Brazilian's auxiliary nurse

This paper presents Brazilian's experience with the organization of methods and strategies for the assessment of competencies for technical level of nursing workers. The evaluative process proposed includes the creation of a learning-oriented and distance-based virtual assessment environment. The proposed methodology for professional competencies assessment adopted a critical-emancipatory perspective. A tele-education environment was deployed, involving software development - a virtual man - and an assessment cybertutor. Learning modules for the cybertutor were developed and videos of clinical simulations, structured around assessment in cognitive, behavioral, and simulation areas. The evaluation modules considered aspects of competencies in know-know, know-how and know-act professional ethics. Also the variability of practices of nursing - hospitals and primary health care units - was considered. This instrument showed as an important strategy for the optimization of assessment procedures that are widely used across Brazil and it is a powerful tool for incorporation into the continuing professional education.

Hierachy-based methodology for producing educational contents with maximal reutilization

Computer based training or distance education are facing dramatic changes withthe advent of standardization efforts, some of them concentrating in maximal reuse.This is of paramount importance for a sustainable -cost affordable- production ofeducational materials. Reuse in itself should not be a goal, though, since manymethodological aspects might be lost. In this paper we propose two contentproduction approaches for the InterMediActor platform under a competence-basedmethodology: either a bottom-up approach where content is designed from scratchor a top-down methodology where existing material can be gradually adapted tofulfil requisites to be used with maximal flexibility into InterMediActor.

Perspectives of Parents of Children with Autism Spectrum Disorder on a Community-Based Parent Education Program

In 2012 a community-based agency that oversees Intensive Behaviour Intervention services for young children diagnosed with Autism Spectrum Disorder (ASD) began delivering newly developed curricula to parents of eligible children. The curricula’s intent was to inform parents about ASD and Applied Behaviour Analysis, to increase their awareness of available community resources, and assist them to be active and engaged in their child’s learning. This mixed-method study used a program-specific survey and focus groups to explore the perspectives parents had on their involvement in these education sessions. Through constant comparison analysis 4 major and 3 minor themes emerged. In general, parents acknowledged that this parent education program included relevant content and a favourable delivery format. The study summarized a number of well-articulated, practical suggestions parents provided. Implications for practice would be applicable to educators interested in providing quality group-based education to parents of young children with ASD.

Teaching Intercultural Communication in Foreign Language Education through Video Conferencing

Since 1980s, Western linguists and specialists on second language acquisition have emphasized the importance of enhancing students’ intercultural communication competence in foreign language education. At the same time, the demand for intercultural communicative competence increased along with the advances of communication technology with its increasingly global reach and the process of globalization itself.In the field of distance language education, these changes have resulted in a shift of focus from the production and distribution of learning materials towards communication and learning as a social process, facilitated by various internet-based platforms. The current focus on learners interacting and communicating synchronously trough videoconferencing is known as the fourth generation of distance language education. Despite the fact that teaching of Chinese as a foreign language (CFL) faces the same or even greater challenges as teaching other languages, the intercultural communication perspective is still quite a new trend in CFL and its implementation and evaluation are still under development. Moreover, the advocates of the new trends in CFL have so far focused almost exclusively on classroom-based courses, neglecting the distance mode of CFL and leaving it as an open field for others to explore. In this under-researched context, Dalarna University (Sweden), where I currently work, started to provide web-based courses of the Chinese language in 2007. Since 2010, the Chinese language courses have been available only in the distance form, using the same teaching materials as the previous campus-based courses. The textbooks used in both settings basically followed the functional nationalism approach. However, in order to catch up with the main trend of foreign-language education, we felt a need to implement the cross-cultural dimension into the distance courses as well. Therefore in 2010, a pilot study has been carried out to explore opportunities and challenges for implementing a cross-cultural perspective into existing courses and evaluating the effectiveness of this implementation based on the feedback of the students and on the experience of the teacher/researcher.

Practice-based film education for children: teaching and learning for creativity, citizenship and participation

Practice-oriented film education aimed at children has been hailed for various reasons: at a personal level, as a means of providing tools for self-expression, for developing creativity and communication skills. And at a social level, it is argued that children must now become competent producers, in addition to critical consumers, of audiovisual content so they can take part in the global public sphere that is arguably emerging. This chapter discusses how the challenges posed by introducing children to filmmaking (i.e. digital video) are being met at three civil associations in Mexico: La Matatena AC, which seeks to enrich the children’s lives by means of the aesthetic experience filmmaking can bring them. Comunicaciòn Comunitaria, concerned with the impact filmmaking can have on the community, preserving cultural memory and enabling participation. And Juguemos a Grabar, with a focus on urban regeneration through the cultural industries.

Reliable detection of directional couplings using rank statistics

To detect directional couplings from time series various measures based on distances in reconstructed state spaces were introduced. These measures can, however, be biased by asymmetries in the dynamics' structure, noise color, or noise level, which are ubiquitous in experimental signals. Using theoretical reasoning and results from model systems we identify the various sources of bias and show that most of them can be eliminated by an appropriate normalization. We furthermore diminish the remaining biases by introducing a measure based on ranks of distances. This rank-based measure outperforms existing distance-based measures concerning both sensitivity and specificity for directional couplings. Therefore, our findings are relevant for a reliable detection of directional couplings from experimental signals.

How geographic distance and depth drive ecological variability and isolation of demersal fish communities in an archipelago system (Cape Verde, Eastern Atlantic Ocean)

Cape Verde is a tropical oceanic ecosystem, highly fragmented and dispersed, with islands physically isolated by distance and depth. To understand how isolation affects the ecological variability in this archipelago, we conducted a research project on the community structure of the 18 commercially most important demersal fishes. An index of ecological distance based on species relative dominance (Di) is developed from Catch Per Unit Effort, derived from an extensive database of artisanal fisheries. Two ecological measures of distance between islands are calculated: at the species level, DDi, and at the community level, DD (sum of DDi). A physical isolation factor (Idb) combining distance (d) and bathymetry (b) is proposed. Covariance analysis shows that isolation factor is positively correlated with both DDi and DD, suggesting that Idb can be considered as an ecological isolation factor. The effect of Idb varies with season and species. This effect is stronger in summer (May to November), than in winter (December to April), which appears to be more unstable. Species react differently to Idb, independently of season. A principal component analysis on the monthly (DDi) for the 12 islands and the 18 species, complemented by an agglomerative hierarchical clustering, shows a geographic pattern of island organization, according to Idb. Results indicate that the ecological structure of demersal fish communities of Cape Verde archipelago, both in time and space, can be explained by a geographic isolation factor. The analytical approach used here is promising and could be tested in other archipelago systems.

IWD to Study the Effect of Prison Education on Employment, Data Download, Iowa Department of Corrections, February 2009

The Iowa Department of Corrections recently entered into a data sharing agreement with Iowa Workforce Development (IWD), the purpose of which is to better ascertain the effect of prison education on postprison employment. This study is important because the DOC partners with community colleges to provide prison-based education, with a goal of increasing the numbers of inmates completing GEDs. We are demonstrating success toward that goal, but what we lack is empirical evidence showing the level of success that Iowa prison education programs have on Iowa offenders’ employment success upon their return to communities here in the state.

The development and pilot-testing of a training curriculum in adolescent medicine and health.

PURPOSE: To select and propose a set of knowledge, attitudes, and skills essential for the care of adolescents; to encourage the development of adolescent health multidisciplinary networks; and to set up training programs in as many European countries as possible. METHODS: The curriculum was developed by 16 physicians from 11 European countries with various professional specializations. In line with modern guidelines in medical education, it is a modular, flexible instrument which covers the main teaching areas in the field, such as basic skills (i.e. setting, rights and confidentiality, gender and cultural issues) as well as specific themes (i.e. sexual and reproductive health, eating disorders, chronic conditions). It consists of 17 thematic modules, each containing detailed objectives, learning approaches, examples, and evaluation methods. RESULT: Two international one-week summer schools were used to assess the feasibility and appropriateness of the curriculum. The overall evaluation was good, with most of the items surpassing three on a four-point Likert scale. However, it pointed to several aspects (process and content) which will need to be refined in the future, such as an increase in interactive sessions (role playing), and a better mix of clinical and public health issues.

Decision-making with distance measures and inducedaggregation operators

[spa] Se presenta un nuevo modelo para la toma de decisiones basado en el uso de medidas de distancia y de operadores de agregación inducidos. Se introduce la distancia media ponderada ordenada inducida (IOWAD). Es un nuevo operador de agregación que extiende el operador OWA a través del uso de distancias y un proceso de reordenación de los argumentos basado en variables de ordenación inducidas. La principal ventaja el operador IOWAD es la posibilidad de utilizar una familia parametrizada de operadores de agregación entre la distancia individual máxima y la mínima. Se estudian algunas de sus principales propiedades y algunos casos particulares. Se desarrolla un ejemplo numérico en un problema de toma de decisiones sobre selección de inversiones. Se observa que la principal ventaja de este modelo en la toma de decisiones es la posibilidad de mostrar una visión más completa del proceso, de forma que el decisor está capacitado para seleccionar la alternativa que está más cerca de sus intereses.

Decision-making with distance measures and inducedaggregation operators

[spa] Se presenta un nuevo modelo para la toma de decisiones basado en el uso de medidas de distancia y de operadores de agregación inducidos. Se introduce la distancia media ponderada ordenada inducida (IOWAD). Es un nuevo operador de agregación que extiende el operador OWA a través del uso de distancias y un proceso de reordenación de los argumentos basado en variables de ordenación inducidas. La principal ventaja el operador IOWAD es la posibilidad de utilizar una familia parametrizada de operadores de agregación entre la distancia individual máxima y la mínima. Se estudian algunas de sus principales propiedades y algunos casos particulares. Se desarrolla un ejemplo numérico en un problema de toma de decisiones sobre selección de inversiones. Se observa que la principal ventaja de este modelo en la toma de decisiones es la posibilidad de mostrar una visión más completa del proceso, de forma que el decisor está capacitado para seleccionar la alternativa que está más cerca de sus intereses.

Genetic diversity in table grapes based on RAPD and microsatellite markers

The objective of this work was to analyze the genetic diversity of 47 table grape accessions, from the grapevine germplasm bank of Embrapa Semiárido, using 20 RAPD and seven microsatellite markers. Genetic distances between pairs of accessions were obtained based on Jaccard's similarity index for RAPD data and on the arithmetic complement of the weighted index for microsatellite data. The groups were formed according to the Tocher's cluster analysis and to the unweighted pair‑group method with arithmetic mean (UPGMA). The microsatellite markers were more efficient than the RAPD ones in the identification of genetic relationships. Information on the genetic distance, based on molecular characteristics and coupled with the cultivar agronomic performance, allowed for the recommendation of parents for crossings, in order to obtain superior hybrids in segregating populations for the table grape breeding program of Embrapa Semiárido.

Development of a systematic computer vision-based method to analyse and compare images of false identity documents for forensic intelligence purposes-Part I: acquisition, calibration and validation issues

Following their detection and seizure by police and border guard authorities, false identity and travel documents are usually scanned, producing digital images. This research investigates the potential of these images to classify false identity documents, highlight links between documents produced by a same modus operandi or same source, and thus support forensic intelligence efforts. Inspired by previous research work about digital images of Ecstasy tablets, a systematic and complete method has been developed to acquire, collect, process and compare images of false identity documents. This first part of the article highlights the critical steps of the method and the development of a prototype that processes regions of interest extracted from images. Acquisition conditions have been fine-tuned in order to optimise reproducibility and comparability of images. Different filters and comparison metrics have been evaluated and the performance of the method has been assessed using two calibration and validation sets of documents, made up of 101 Italian driving licenses and 96 Portuguese passports seized in Switzerland, among which some were known to come from common sources. Results indicate that the use of Hue and Edge filters or their combination to extract profiles from images, and then the comparison of profiles with a Canberra distance-based metric provides the most accurate classification of documents. The method appears also to be quick, efficient and inexpensive. It can be easily operated from remote locations and shared amongst different organisations, which makes it very convenient for future operational applications. The method could serve as a first fast triage method that may help target more resource-intensive profiling methods (based on a visual, physical or chemical examination of documents for instance). Its contribution to forensic intelligence and its application to several sets of false identity documents seized by police and border guards will be developed in a forthcoming article (part II).