Quest for Orthologs Entails Quest for Tree of Life: In Search of the Gene Stream.

Quest for Orthologs (QfO) is a community effort with the goal to improve and benchmark orthology predictions. As quality assessment assumes prior knowledge on species phylogenies, we investigated the congruency between existing species trees by comparing the relationships of 147 QfO reference organisms from six Tree of Life (ToL)/species tree projects: The National Center for Biotechnology Information (NCBI) taxonomy, Opentree of Life, the sequenced species/species ToL, the 16S ribosomal RNA (rRNA) database, and trees published by Ciccarelli et al. (Ciccarelli FD, et al. 2006. Toward automatic reconstruction of a highly resolved tree of life. Science 311:1283-1287) and by Huerta-Cepas et al. (Huerta-Cepas J, Marcet-Houben M, Gabaldon T. 2014. A nested phylogenetic reconstruction approach provides scalable resolution in the eukaryotic Tree Of Life. PeerJ PrePrints 2:223) Our study reveals that each species tree suggests a different phylogeny: 87 of the 146 (60%) possible splits of a dichotomous and rooted tree are congruent, while all other splits are incongruent in at least one of the species trees. Topological differences are observed not only at deep speciation events, but also within younger clades, such as Hominidae, Rodentia, Laurasiatheria, or rosids. The evolutionary relationships of 27 archaea and bacteria are highly inconsistent. By assessing 458,108 gene trees from 65 genomes, we show that consistent species topologies are more often supported by gene phylogenies than contradicting ones. The largest concordant species tree includes 77 of the QfO reference organisms at the most. Results are summarized in the form of a consensus ToL (http://swisstree.vital-it.ch/species_tree) that can serve different benchmarking purposes.

Trust region versus line search for computing the optical flow

We consider the numerical treatment of the optical flow problem by evaluating the performance of the trust region method versus the line search method. To the best of our knowledge, the trust region method is studied here for the first time for variational optical flow computation. Four different optical flow models are used to test the performance of the proposed algorithm combining linear and nonlinear data terms with quadratic and TV regularization. We show that trust region often performs better than line search; especially in the presence of non-linearity and non-convexity in the model.

Search Interfaces on the Web: Querying and Characterizing

Current-day web search engines (e.g., Google) do not crawl and index a significant portion of theWeb and, hence, web users relying on search engines only are unable to discover and access a large amount of information from the non-indexable part of the Web. Specifically, dynamic pages generated based on parameters provided by a user via web search forms (or search interfaces) are not indexed by search engines and cannot be found in searchers’ results. Such search interfaces provide web users with an online access to myriads of databases on the Web. In order to obtain some information from a web database of interest, a user issues his/her query by specifying query terms in a search form and receives the query results, a set of dynamic pages that embed required information from a database. At the same time, issuing a query via an arbitrary search interface is an extremely complex task for any kind of automatic agents including web crawlers, which, at least up to the present day, do not even attempt to pass through web forms on a large scale. In this thesis, our primary and key object of study is a huge portion of the Web (hereafter referred as the deep Web) hidden behind web search interfaces. We concentrate on three classes of problems around the deep Web: characterization of deep Web, finding and classifying deep web resources, and querying web databases. Characterizing deep Web: Though the term deep Web was coined in 2000, which is sufficiently long ago for any web-related concept/technology, we still do not know many important characteristics of the deep Web. Another matter of concern is that surveys of the deep Web existing so far are predominantly based on study of deep web sites in English. One can then expect that findings from these surveys may be biased, especially owing to a steady increase in non-English web content. In this way, surveying of national segments of the deep Web is of interest not only to national communities but to the whole web community as well. In this thesis, we propose two new methods for estimating the main parameters of deep Web. We use the suggested methods to estimate the scale of one specific national segment of the Web and report our findings. We also build and make publicly available a dataset describing more than 200 web databases from the national segment of the Web. Finding deep web resources: The deep Web has been growing at a very fast pace. It has been estimated that there are hundred thousands of deep web sites. Due to the huge volume of information in the deep Web, there has been a significant interest to approaches that allow users and computer applications to leverage this information. Most approaches assumed that search interfaces to web databases of interest are already discovered and known to query systems. However, such assumptions do not hold true mostly because of the large scale of the deep Web – indeed, for any given domain of interest there are too many web databases with relevant content. Thus, the ability to locate search interfaces to web databases becomes a key requirement for any application accessing the deep Web. In this thesis, we describe the architecture of the I-Crawler, a system for finding and classifying search interfaces. Specifically, the I-Crawler is intentionally designed to be used in deepWeb characterization studies and for constructing directories of deep web resources. Unlike almost all other approaches to the deep Web existing so far, the I-Crawler is able to recognize and analyze JavaScript-rich and non-HTML searchable forms. Querying web databases: Retrieving information by filling out web search forms is a typical task for a web user. This is all the more so as interfaces of conventional search engines are also web forms. At present, a user needs to manually provide input values to search interfaces and then extract required data from the pages with results. The manual filling out forms is not feasible and cumbersome in cases of complex queries but such kind of queries are essential for many web searches especially in the area of e-commerce. In this way, the automation of querying and retrieving data behind search interfaces is desirable and essential for such tasks as building domain-independent deep web crawlers and automated web agents, searching for domain-specific information (vertical search engines), and for extraction and integration of information from various deep web resources. We present a data model for representing search interfaces and discuss techniques for extracting field labels, client-side scripts and structured data from HTML pages. We also describe a representation of result pages and discuss how to extract and store results of form queries. Besides, we present a user-friendly and expressive form query language that allows one to retrieve information behind search interfaces and extract useful data from the result pages based on specified conditions. We implement a prototype system for querying web databases and describe its architecture and components design.

Question Waves: A multicast query routing algorithm for social search

This paper describes Question Waves, an algorithm that can be applied to social search protocols, such as Asknext or Sixearch. In this model, the queries are propagated through the social network, with faster propagation through more trustable acquaintances. Question Waves uses local information to make decisions and obtain an answer ranking. With Question Waves, the answers that arrive first are the most likely to be relevant, and we computed the correlation of answer relevance with the order of arrival to demonstrate this result. We obtained correlations equivalent to the heuristics that use global knowledge, such as profile similarity among users or the expertise value of an agent. Because Question Waves is compatible with the social search protocol Asknext, it is possible to stop a search when enough relevant answers have been found; additionally, stopping the search early only introduces a minimal risk of not obtaining the best possible answer. Furthermore, Question Waves does not require a re-ranking algorithm because the results arrive sorted

Search and Discovery : OER's Open Loop

Open educational resources (OER) promise increased access, participation, quality, and relevance, in addition to cost reduction. These seemingly fantastic promises are based on the supposition that educators and learners will discover existing resources, improve them, and share the results, resulting in a virtuous cycle of improvement and re-use. By anecdotal metrics, existing web scale search is not working for OER. This situation impairs the cycle underlying the promise of OER, endangering long term growth and sustainability. While the scope of the problem is vast, targeted improvements in areas of curation, indexing, and data exchange can improve the situation, and create opportunities for further scale. I explore the way the system is currently inadequate, discuss areas for targeted improvement, and describe a prototype system built to test these ideas. I conclude with suggestions for further exploration and development.

Cost Optimisation of Mobile Advertising Client Data Transfer

Data traffic caused by mobile advertising client software when it is communicating with the network server can be a pain point for many application developers who are considering advertising-funded application distribution, since the cost of the data transfer might scare their users away from using the applications. For the thesis project, a simulation environment was built to mimic the real client-server solution for measuring the data transfer over varying types of connections with different usage scenarios. For optimising data transfer, a few general-purpose compressors and XML-specific compressors were tried for compressing the XML data, and a few protocol optimisations were implemented. For optimising the cost, cache usage was improved and pre-loading was enhanced to use free connections to load the data. The data traffic structure and the various optimisations were analysed, and it was found that the cache usage and pre-loading should be enhanced and that the protocol should be changed, with report aggregation and compression using WBXML or gzip.

Decomposição catalítica de óxidos de nitrogênio

Contaminant gases in the atmosphere constitute an important problem to be solved in the world. The NOx gases produced as a consequence of engine high temperatures are deleterious to environment and human health, as they promote acid rain and can act in the same way as freons in the destruction of the ozone layer in the stratosphere. In this review, three way and selective reduction catalysts for decomposition of these contaminant gases are described. Details about conditions and problems, such as catalyst poisoning, and the search for new catalysts are shown.

The Influence of the media and advertising on eating disorders

This article describes a literature review of the influence of advertising and the media on Eating Disorders (ED). Research published in scientific journals in various fields of social sciences such as sychology, psychiatry and communication science has enabled us to conclude that the content displayed in the media, including advertising, are enhancers of disorders and contribute significantly to body issatisfaction in relation to the perceived idea of beauty, it also facilitates the development of weight loss strategies in women and gain of muscle mass in men.

Periodismo y dispositivos móviles de lecto-escritura. Introducción al diseño de contenidos para tabletas

El lanzamiento de las tabletas, especialmente la iPad de Apple en 2010, abrió la competencia entre las compañías de comunicación en el sentido de hacer disponible el contenido para este entorno de medios emergentes. La fuga de lectores de periódicos impresos y la consecuente caída en las ganancias por publicidad, forzó a las compañías periodísticas a que buscaran los otros medios de mantener sus negocios. La diversificación de productos y la penetración de los periódicos en dispositivos móviles constituyen un escenario prometedor para el medio. El vertiginoso volumen de ventas de las tabletas indica que en 2012 serán comercializadas más de 140 millones de unidades en el mundo. El diseño de los periódicos en tabletas está íntimamente ligado al diseño de la versión impresa por la fuerza de su metáfora. El desafío es encontrar un diseño de páginas propio, aprovechando el potencial multimedia sin interferir negativamente en la legibilidad y en el carácter intrínseco de informar.

Consumer Search Behavior in High Involvement Purchases

The aim of this study is to investigate the consumer search behavior in high involvement purchases. The results of this research provide the descriptive analysis of the information search phase which is a part of the decision-making process. The study focuses on customer’s choice of the information sources, motivation behind it and different factors that influence the search behavior. Particular attention is paid to the purchase categorization and the differences in information search between products and services. The qualitative research method is chosen for this study. The data is gathered through ten theme interviews. Each participant of the interview describes his/her own search behavior in a product and a service case. The results indicate that consumer search behavior vary according to the purchase categorization, demographic, individual and situational factors. Moreover, the above-mentioned factors influence the purpose and position of the information search phase in a five-step decision making model.

Web-sovellus Google App Engine alustalle

App Engine on lyhenne englanninkielisistä termeistä application, sovellus ja engine, moottori. Kyseessä on Google, Inc. -konsernin toteuttama kaupallinen palvelu, joka noudattaa pilvimallin tietojenkäsittelyn periaatteita ja mahdollistaa asiakkaan oman sovelluskehityksen. Järjestelmään on mahdollista ohjelmoida itse ideoitu palvelu Internet - verkon välityksellä käytettäväksi, joko yksityisesti tai julkisesti. Kyse on siis hajautetusta palvelinjärjestelmästä, jonka tarjoaa dynaamisesti kuormitukseen sopeutuvan sovellusalustan, jossa asiakas ei vuokraa virtuaalikoneita. Myös järjestelmän tarjoama tallennuskapasiteetti on saatavilla joustavasti. Itse kandidaatintyössä syvennytään yksityiskohtaisemmin sovelluksen toteuttamiseen palvelussa, rajoitteisiin ja soveltuvuuteen. Alussa käydään läpi pilvikäsite, joista monilla tietokoneiden käyttäjillä on epäselvä käsitys. Erilaisia kokonaisuuksia voidaan luoda erittäin monella tavalla, joista rajaamme käsittelyn kohteeksi toteuttamiskelpoiset yleiset ratkaisut.

In search of true friendship

The present text proposes a discussion on the concept of true friendship. The argument is grounded mostly on Aristotle's Nicomachean Ethics, Owen Flanagan's ethics as human ecology, and on contemporary authors' works about the Greek philosopher's concept of friendship. Given that human beings flourish through 1) exercising capacities, 2) being moral, and 3) having true friendships, difficulties to establish the level of trust required by true friendships turns the search itself (for them) morally valid.