Development of computational tools for the integrated analysis of DNA microarray data with applications in cancer research

The MAP-i Doctoral Program of the Universities of Minho, Aveiro and Porto

Biana: a software framework for compiling biological interactions and analyzing networks

Background: The analysis and usage of biological data is hindered by the spread of information across multiple repositories and the difficulties posed by different nomenclature systems and storage formats. In particular, there is an important need for data unification in the study and use of protein-protein interactions. Without good integration strategies, it is difficult to analyze the whole set of available data and its properties.Results: We introduce BIANA (Biologic Interactions and Network Analysis), a tool for biological information integration and network management. BIANA is a Python framework designed to achieve two major goals: i) the integration of multiple sources of biological information, including biological entities and their relationships, and ii) the management of biological information as a network where entities are nodes and relationships are edges. Moreover, BIANA uses properties of proteins and genes to infer latent biomolecular relationships by transferring edges to entities sharing similar properties. BIANA is also provided as a plugin for Cytoscape, which allows users to visualize and interactively manage the data. A web interface to BIANA providing basic functionalities is also available. The software can be downloaded under GNU GPL license from http://sbi.imim.es/web/BIANA.php.Conclusions: BIANA's approach to data unification solves many of the nomenclature issues common to systems dealing with biological data. BIANA can easily be extended to handle new specific data repositories and new specific data types. The unification protocol allows BIANA to be a flexible tool suitable for different user requirements: non-expert users can use a suggested unification protocol while expert users can define their own specific unification rules.

The Development of Weak Signal Concept

Tämän hetken trendit kuten globalisoituminen, ympäristömme turbulenttisuus, elintason nousu, turvallisuuden tarpeen kasvu ja teknologian kehitysnopeus korostavatmuutosten ennakoinnin tarpeellisuutta. Pysyäkseen kilpailukykyisenä yritysten tulee kerätä, analysoida ja hyödyntää liiketoimintatietoa, jokatukee niiden toimintaa viranomaisten, kilpailijoiden ja asiakkaiden toimenpiteiden ennakoinnissa. Innovoinnin ja uusien konseptien kehittäminen, kilpailijoiden toiminnan arviointi, asiakkaiden tarpeet muun muassa vaativatennakoivaa arviointia. Heikot signaalit ovat keskeisessä osassa organisaatioiden valmistautumisessa tulevaisuuden tapahtumiin. Opinnäytetyön tarkoitus on luoda ja kehittää heikkojen signaalien ymmärrystä ja hallintaa sekäkehittää konseptuaalinen ja käytännöllinen lähestymistapa ennakoivan toiminnan edistämiselle. Heikkojen signaalien tyyppien luokittelu perustuu ominaisuuksiin ajan, voimakkuuden ja liiketoimintaan integroinnin suhteen. Erityyppiset heikot signaalit piirteineen luovat reunaehdot laatutekijöiden keräämiselle ja siitä edelleen laatujärjestelmän ja matemaattiseen malliin perustuvan työvälineen kehittämiselle. Heikkojen signaalien laatutekijät on kerätty yhteen kaikista heikkojen signaalien konseptin alueista. Analysoidut ja kohdistetut laatumuuttujat antavat mahdollisuuden kehittää esianalyysiä ja ICT - työvälineitä perustuen matemaattisen mallin käyttöön. Opinnäytetyön tavoitteiden saavuttamiseksi tehtiin ensin Business Intelligence -kirjallisuustutkimus. Hiekkojen signaalien prosessi ja systeemi perustuvat koottuun Business Intelligence - systeemiin. Keskeisinä kehitysalueina tarkasteltiin liiketoiminnan integraatiota ja systemaattisen menetelmän kehitysaluetta. Heikkojen signaalien menetelmien ja määritelmien kerääminen sekä integrointi määriteltyyn prosessiin luovat uuden konseptin perustan, johon tyypitys ja laatutekijät kytkeytyvät. Käytännöllisen toiminnan tarkastelun ja käyttöönoton mahdollistamiseksi toteutettiin Business Intelligence markkinatutkimus (n=156) sekä yhteenveto muihin saatavilla oleviin markkinatutkimuksiin. Syvähaastatteluilla (n=21) varmennettiin laadullisen tarkastelun oikeellisuus. Lisäksi analysoitiin neljä käytännön projektia, joiden yhteenvedot kytkettiin uuden konseptin kehittämiseen. Prosessi voidaan jakaa kahteen luokkaan: yritysten markkinasignaalit vuoden ennakoinnilla ja julkisen sektorin verkostoprojektit kehittäen ennakoinnin struktuurin luonnin 7-15 vuoden ennakoivalle toiminnalle. Tutkimus rajattiin koskemaan pääasiassa ulkoisen tiedon aluetta. IT työvälineet ja lopullisen laatusysteemin kehittäminen jätettiin tutkimuksen ulkopuolelle. Opinnäytetyön tavoitteena ollut heikkojen signaalien konseptin kehittäminen toteutti sille asetetut odotusarvot. Heikkojen signaalien systemaattista tarkastelua ja kehittämistyötä on mahdollista edistää Business Intelligence - systematiikan hyödyntämisellä. Business Intelligence - systematiikkaa käytetään isojen yritysten liiketoiminnan suunnittelun tukena.Organisaatioiden toiminnassa ei ole kuitenkaan yleisesti hyödynnetty laadulliseen analyysiin tukeutuvaa ennakoinnin weak signals - toimintaa. Ulkoisenja sisäisen tiedon integroinnin ja systematiikan hyödyt PK -yritysten tukena vaativat merkittävää panostusta julkishallinnon rahoituksen ja kehitystoiminnan tukimuotoina. Ennakointi onkin tuottanut lukuisia julkishallinnon raportteja, mutta ei käytännön toteutuksia. Toisaalta analysoitujen case-tapausten tuloksena voidaan nähdä, ettei organisaatioissa välttämättä tarvita omaa projektipäällikköä liiketoiminnan tuen kehittämiseksi. Business vastuun ottamiseksi ja asiaan sitoutumiseen on kuitenkin löydyttävä oikea henkilö

Toimitusketjun kehittäminen tukkujakelukanavassa

Asiakaslähtöinen liiketoimintatapa on voimakkaasti valtaamassa alaa tuote- ja tuotanto-orientoituneelta. Tuotteiden erinomaisuus koetaan markkinoilla yhä enenevässä määrin itsestään selvyydeksi. Prosessien tehokas hallitseminen ja asiakkaan kokeman lisäarvon muodostaminen ovat muodostuneet ratkaisevimmaksi kilpailuedun luojaksi. Toimitusketjun hallinnalla on tämän kilpailuedun muodostumisessa ratkaiseva rooli. Diplomityö käsittelee toimitusketjun hallinnan tarjoamia mahdollisuuksia kehittää kohdeyrityksen tukkujakelukanavaa. Työssä pureudutaan toimitusketjun ohjauksen ja sähköisen liiketoiminnan mukanaan tuomien mahdollisuuksien hyödyntämiseen. Tärkeinä kehitystyön menetelminä esitetään toimitusketjun yhteistyön tiivistäminen ja informaation integraatio sekä näiden merkitys toimitusketjussa esiintyvän kysynnän piiskavaikutuksen vähentämiseksi.Työn empiirisen osan tuloksena on luotu kuvaus tutkitusta jakelukanavasta välillä loppuasiakas – kohdeyritys, sen toimitusketjun ohjauksesta ja toteutuneesta toiminnasta. Tämän perusteella on jakelukanavalle luotu kehitysmalli. Malli pitää sisällään viitekehyksen toimitusketjun ohjaukselle, käytännön toimenpide-ehdotukset ja saavutettavien hyötyjen arvioinnin.

Effects of isoflavone on the learning and memory of women in menopause: a double-blind placebo-controlled study

Hormone decline is common to all women during aging and, associated with other factors, leads to cognitive impairment. Its replacement enhances cognitive performance, but not all women present a clinical and family or personal history that justifies its use, mainly women with a history of cancer. The aim of this study was to determine whether a daily oral dose of 80 mg of isoflavone extract for 4 months can produce benefits in women with low hormone levels, contributing to improvement in cognitive aspects. The sample comprised 50- to 65-year-old women whose menstruation had ceased at least 1 year before and who had not undergone hormone replacement. The volunteers were allocated to two groups of 19 individuals each, i.e., isoflavone and placebo. There was a weak correlation between menopause duration and low performance in the capacity to manipulate information (central executive). We observed an increase in the capacity to integrate information in the group treated with isoflavone, but no improvement in the capacity to form new memories. We did not observe differences between groups in terms of signs and symptoms suggestive of depression according to the Geriatric Depression Scale. Our results point to a possible beneficial effect of isoflavone on some abilities of the central executive. These effects could also contribute to minimizing the impact of memory impairment. Further research based on controlled clinical trials is necessary to reach consistent conclusions.

Las TIC en la administración de la cadena de suministro y su incidencia en el desempeño operacional

Las tecnologías de la información han empezado a ser un factor importante a tener en cuenta en cada uno de los procesos que se llevan a cabo en la cadena de suministro. Su implementación y correcto uso otorgan a las empresas ventajas que favorecen el desempeño operacional a lo largo de la cadena. El desarrollo y aplicación de software han contribuido a la integración de los diferentes miembros de la cadena, de tal forma que desde los proveedores hasta el cliente final, perciben beneficios en las variables de desempeño operacional y nivel de satisfacción respectivamente. Por otra parte es importante considerar que su implementación no siempre presenta resultados positivos, por el contrario dicho proceso de implementación puede verse afectado seriamente por barreras que impiden maximizar los beneficios que otorgan las TIC.

Transparent access to relational, autonomous and distributed databases using semantic web and service oriented technologies

With the constant grow of enterprises and the need to share information across departments and business areas becomes more critical, companies are turning to integration to provide a method for interconnecting heterogeneous, distributed and autonomous systems. Whether the sales application needs to interface with the inventory application, the procurement application connect to an auction site, it seems that any application can be made better by integrating it with other applications. Integration between applications can face several troublesome due the fact that applications may not have been designed and implemented having integration in mind. Regarding to integration issues, two tier software systems, composed by the database tier and by the “front-end” tier (interface), have shown some limitations. As a solution to overcome the two tier limitations, three tier systems were proposed in the literature. Thus, by adding a middle-tier (referred as middleware) between the database tier and the “front-end” tier (or simply referred application), three main benefits emerge. The first benefit is related with the fact that the division of software systems in three tiers enables increased integration capabilities with other systems. The second benefit is related with the fact that any modifications to the individual tiers may be carried out without necessarily affecting the other tiers and integrated systems and the third benefit, consequence of the others, is related with less maintenance tasks in software system and in all integrated systems. Concerning software development in three tiers, this dissertation focus on two emerging technologies, Semantic Web and Service Oriented Architecture, combined with middleware. These two technologies blended with middleware, which resulted in the development of Swoat framework (Service and Semantic Web Oriented ArchiTecture), lead to the following four synergic advantages: (1) allow the creation of loosely-coupled systems, decoupling the database from “front-end” tiers, therefore reducing maintenance; (2) the database schema is transparent to “front-end” tiers which are aware of the information model (or domain model) that describes what data is accessible; (3) integration with other heterogeneous systems is allowed by providing services provided by the middleware; (4) the service request by the “frontend” tier focus on ‘what’ data and not on ‘where’ and ‘how’ related issues, reducing this way the application development time by developers.

Effects of isoflavone on the learning and memory of women in menopause: a double-blind placebo-controlled study

Hormone decline is common to all women during aging and, associated with other factors, leads to cognitive impairment. Its replacement enhances cognitive performance, but not all women present a clinical and family or personal history that justifies its use, mainly women with a history of cancer. The aim of this study was to determine whether a daily oral dose of 80 mg of isoflavone extract for 4 months can produce benefits in women with low hormone levels, contributing to improvement in cognitive aspects. The sample comprised 50- to 65-year-old women whose menstruation had ceased at least 1 year before and who had not undergone hormone replacement. The volunteers were allocated to two groups of 19 individuals each, i.e., isoflavone and placebo. There was a weak correlation between menopause duration and low performance in the capacity to manipulate information (central executive). We observed an increase in the capacity to integrate information in the group treated with isoflavone, but no improvement in the capacity to form new memories. We did not observe differences between groups in terms of signs and symptoms suggestive of depression according to the Geriatric Depression Scale. Our results point to a possible beneficial effect of isoflavone on some abilities of the central executive. These effects could also contribute to minimizing the impact of memory impairment. Further research based on controlled clinical trials is necessary to reach consistent conclusions.

Analog Modeling of Human Cognitive Functions with Tripartite Synapses

Searching for an understanding of how the brain supports conscious processes, cognitive scientists have proposed two main classes of theory: Global Workspace and Information Integration theories. These theories seem to be complementary, but both still lack grounding in terms of brain mechanisms responsible for the production of coherent and unitary conscious states. Here we propose following James Robertson's "Astrocentric Hypothesis" - that conscious processing is based on analog computing in astrocytes. The "hardware" for these computations is calcium waves mediated by adenosine triphosphate signaling. Besides presenting our version of this hypothesis, we also review recent findings on astrocyte morphology that lend support to their functioning as Local Hubs (composed of protoplasmic astrocytes) that integrate synaptic activity, and as a Master Hub (composed, in the human brain, by a combination of interlaminar, fibrous, polarized and varicose projection astrocytes) that integrates whole-brain activity.

A importância das informações aferentes podais para o controle postural

Introduction. The postural control involves a complex mechanism for connecting the afferent and efferent pathways and their integration into the central nervous system (CNS). Three systems are responsible to obtain outside information: visual, vestibular and sensory. Recent studies have shown that among such systems, the CNS shows a greater predilection for sensory information to postural control. Objective. Given this, the review proposes to discuss the feet sensory information importance and its reflection in postural control mechanisms. Method. For this reason, a literature search was carried out by PubMed and Bireme libraries, and papers of the last five years were selected. Specific books were also used. Discussion. Studies were separated into topics on sensory information integration to neuro-motor answer, postural feed-forward adjustments recruitment mechanisms; neuro-muscular coordination and synergy responses and the musculoskeletal tissues role. Conclusion. Despite has been found a large number of studies, the real mechanism that the CNS uses to filter, integrate and process the sensory information and select the appropriate motor response, be it for the movement or posture for the stabilization remains obscure.

The service bundle design in a digital environment

Der Artikel behandelt das Projektieren der Produkt-Service-Verbindung vom Standpunkt der Informationsintegration aus. Der Autor erläutert grundlegende Unterschiede zwischen dem traditionellen und dem modernen Operationsmanagementkonzept. Ergänzend wird die Rolle der logistischen Unterstüzungsanalyse wird betrachtet. Der Artikel stellt das Konzept von CALS (Continuous Acquisition and Life cycle Support) dar, welches als Umgebung, die Datenverteilung zwischen den in den Entwicklungsprozess beteiligten Geschäftspartnern ermöglicht.

A Conceptual Model to Combine Creativity Techniques with Fuzzy Cognitive Maps for Enhanced Knowledge Management

This chapter introduces a conceptual model to combine creativity techniques with fuzzy cognitive maps (FCMs) and aims to support knowledge management methods by improving expert knowledge acquisition and aggregation. The aim of the conceptual model is to represent acquired knowledge in a manner that is as computer-understandable as possible with the intention of developing automated reasoning in the future as part of intelligent information systems. The formal represented knowledge thus may provide businesses with intelligent information integration. To this end, we introduce and evaluate various creativity techniques with a list of attributes to define the most suitable to combine with FCMs. This proposed combination enables enhanced knowledge management through the acquisition and representation of expert knowledge with FCMs. Our evaluation indicates that the creativity technique known as mind mapping is the most suitable technique in our set. Finally, a scenario from stakeholder management demonstrates the combination of mind mapping with FCMs as an integrated system.

Individual group efficacy beliefs and performance motivation: A mediational approach

Introduction: According to the theoretical model of Cranach, Ochsenbein, and Valach (1986) understanding group actions needs consideration of aspects at both the group level and the level of individual members. For example individual action units constituting group actions are motivated at the individual level while potentially being affected by characteristics of the group. Theoretically, group efficacy beliefs could be a part of this motivational process as they are an individual’s cognitive contents about group-level abilities to perform well in a specific task. Positive relations between group level efficacy-beliefs and group performance have been reported and Bandura and Locke (2003) argue that this relationship is being mediated by motivational processes and goal setting. The aims of this study were a) to examine the effects of group characteristics on individual performance motivation and b) to test if those are mediated by individual group efficacy beliefs. Methods: Forty-seven students (M=22.83 years, SD=2.83, 34% women) of the university of Berne participated in this scenario based experiment. Data were collected on two collection points. Subjects were provided information about fictive team members with whom they had to perform a group triathlon. Three values (low, medium, high) of the other team members’ abilities to perform in their parts of the triathlon (swimming and biking respectively) were combined in a 3x3 full factorial design (Anderson, 1982) yielding nine groups. Subjects were asked how confident they were that the teams would perform well in the task (individual group efficacy beliefs), and to provide information about their motivation to perform at their best in the respective group contexts (performance motivation). Multilevel modeling (Mplus) was used to estimate the effects of the factors swim and bike, and the context-varying covariate individual group efficacy beliefs on performance motivation. Further analyses were undertaken to test if the effects of group contexts on performance motivation are mediated by individual group efficacy beliefs. Results: Significant effects were reported for both the group characteristics (βswim = 7.86; βbike = 8.57; both p < .001) and the individual group efficacy beliefs (βigeb; .40, p < .001) on performance motivation. The subsequent mediation model indicated that the effects of group characteristics on performance motivation were partly mediated by the individual group efficacy beliefs of the subjects with significant mediation effects for both factors swim and bike. Discussion/Conclusion: The results of the study provide further support for the motivational character of efficacy beliefs and point out a mechanism by which team characteristics influence performance relevant factors at the level of individual team members. The study indicates that high team abilities lead to augmented performance motivation, adding a psychological advantage to teams already high on task relevant abilities. Future investigations will be aiming at possibilities to keep individual performance motivation high in groups with low task relevant abilities. One possibility could be the formulation of individual task goals. References: Anderson, N. H. (1982). Methods of information integration theory. New York: Academic Press. Bandura, A. & Locke, E. A. (2003). Negative self-efficacy and goal effects revisited. Journal of Applied Psychology, 88, 87-99. Cranach, M. von, Ochsenbein, G. & Valach, L. (1986). The group as a self-active system: Outline of a theory of group action. European Journal of Social Psychology, 16, 193-229.

Cerebellar Pathology Does Not Impair Performance on Identification or Categorization Tasks

In comparison to the basal ganglia, prefrontal cortex, and medial temporal lobes, the cerebellum has been absent from recent research on the neural substrates of categorization and identification, two prominent tasks in the learning and memory literature. To investigate the contribution of the cerebellum to these tasks, we tested patients with cerebellar pathology (seven with bilateral degeneration, six with unilateral lesions, and two with midline damage) on rule-based and information-integration categorization tasks and an identification task. In rule-based tasks, it is assumed that participants learn the categories through an explicit reasoning process. In information-integration tasks, optimal performance requires the integration of information from multiple stimulus dimensions, and participants are typically unaware of the decision strategy. The identification task, in contrast, required participants to learn arbitrary, color-word associations. The cerebellar patients performed similar to matched controls on all three tasks and performance did not vary with the extent of cerebellar pathology. Although the interpretation of these null results requires caution, these data contribute to the current debate on cerebellar contributions to cognition by providing boundary conditions on understanding the neural substrates of categorization and identification, and help define the functional domain of the cerebellum in learning and memory.

BIOMEDICAL LANGUAGE UNDERSTANDING AND EXTRACTION (BLUE-TEXT): A MINIMAL SYNTACTIC, SEMANTIC METHOD

Clinical text understanding (CTU) is of interest to health informatics because critical clinical information frequently represented as unconstrained text in electronic health records are extensively used by human experts to guide clinical practice, decision making, and to document delivery of care, but are largely unusable by information systems for queries and computations. Recent initiatives advocating for translational research call for generation of technologies that can integrate structured clinical data with unstructured data, provide a unified interface to all data, and contextualize clinical information for reuse in multidisciplinary and collaborative environment envisioned by CTSA program. This implies that technologies for the processing and interpretation of clinical text should be evaluated not only in terms of their validity and reliability in their intended environment, but also in light of their interoperability, and ability to support information integration and contextualization in a distributed and dynamic environment. This vision adds a new layer of information representation requirements that needs to be accounted for when conceptualizing implementation or acquisition of clinical text processing tools and technologies for multidisciplinary research. On the other hand, electronic health records frequently contain unconstrained clinical text with high variability in use of terms and documentation practices, and without commitmentto grammatical or syntactic structure of the language (e.g. Triage notes, physician and nurse notes, chief complaints, etc). This hinders performance of natural language processing technologies which typically rely heavily on the syntax of language and grammatical structure of the text. This document introduces our method to transform unconstrained clinical text found in electronic health information systems to a formal (computationally understandable) representation that is suitable for querying, integration, contextualization and reuse, and is resilient to the grammatical and syntactic irregularities of the clinical text. We present our design rationale, method, and results of evaluation in processing chief complaints and triage notes from 8 different emergency departments in Houston Texas. At the end, we will discuss significance of our contribution in enabling use of clinical text in a practical bio-surveillance setting.