SwissTargetPrediction: a web server for target prediction of bioactive small molecules.

Bioactive small molecules, such as drugs or metabolites, bind to proteins or other macro-molecular targets to modulate their activity, which in turn results in the observed phenotypic effects. For this reason, mapping the targets of bioactive small molecules is a key step toward unraveling the molecular mechanisms underlying their bioactivity and predicting potential side effects or cross-reactivity. Recently, large datasets of protein-small molecule interactions have become available, providing a unique source of information for the development of knowledge-based approaches to computationally identify new targets for uncharacterized molecules or secondary targets for known molecules. Here, we introduce SwissTargetPrediction, a web server to accurately predict the targets of bioactive molecules based on a combination of 2D and 3D similarity measures with known ligands. Predictions can be carried out in five different organisms, and mapping predictions by homology within and between different species is enabled for close paralogs and orthologs. SwissTargetPrediction is accessible free of charge and without login requirement at http://www.swisstargetprediction.ch.

Splitting statistical potentials into meaningful scoring functions: testing the prediction of near-native structures from decoy conformations

Background: Recent advances on high-throughput technologies have produced a vast amount of protein sequences, while the number of high-resolution structures has seen a limited increase. This has impelled the production of many strategies to built protein structures from its sequence, generating a considerable amount of alternative models. The selection of the closest model to the native conformation has thus become crucial for structure prediction. Several methods have been developed to score protein models by energies, knowledge-based potentials and combination of both.Results: Here, we present and demonstrate a theory to split the knowledge-based potentials in scoring terms biologically meaningful and to combine them in new scores to predict near-native structures. Our strategy allows circumventing the problem of defining the reference state. In this approach we give the proof for a simple and linear application that can be further improved by optimizing the combination of Zscores. Using the simplest composite score () we obtained predictions similar to state-of-the-art methods. Besides, our approach has the advantage of identifying the most relevant terms involved in the stability of the protein structure. Finally, we also use the composite Zscores to assess the conformation of models and to detect local errors.Conclusion: We have introduced a method to split knowledge-based potentials and to solve the problem of defining a reference state. The new scores have detected near-native structures as accurately as state-of-art methods and have been successful to identify wrongly modeled regions of many near-native conformations.

@neurIST infrastructure for advanced disease management through integration of heterogeneous data, computing, and complex processing services

The increasing volume of data describing humandisease processes and the growing complexity of understanding, managing, and sharing such data presents a huge challenge for clinicians and medical researchers. This paper presents the@neurIST system, which provides an infrastructure for biomedical research while aiding clinical care, by bringing together heterogeneous data and complex processing and computing services. Although @neurIST targets the investigation and treatment of cerebral aneurysms, the system’s architecture is generic enough that it could be adapted to the treatment of other diseases.Innovations in @neurIST include confining the patient data pertaining to aneurysms inside a single environment that offers cliniciansthe tools to analyze and interpret patient data and make use of knowledge-based guidance in planning their treatment. Medicalresearchers gain access to a critical mass of aneurysm related data due to the system’s ability to federate distributed informationsources. A semantically mediated grid infrastructure ensures that both clinicians and researchers are able to seamlessly access andwork on data that is distributed across multiple sites in a secure way in addition to providing computing resources on demand forperforming computationally intensive simulations for treatment planning and research.

Reporting intellectual capital in Spain

This study reports on the analysis of annual reports from 14- listed companies in Spainover a five-year period, from 1998 to 2002. Companies in the sample are selected on thebasis of their knowledge-based assets and incentives to report on Intellectual Capital.The empirical analysis is twofold:1) Firstly, we analyse the value of intellectual capital using a value-based approach,through the difference between market and book value over the period considered. Results show that there is a general decrease in the 'hidden value' of these companies, probably due to the general trend in stock markets.2) Secondly, we carry out a content-based analysis of the complete annual reports of the companies over the five year period. Preliminary findings seem to suggest that although the level of disclosure has increased over time, this is mainly in the form of narrative. Overall, the level of disclosure of intellectual capital remains low.

A transnacionalização das políticas educativas : itinerários da cooperação portuguesa em Cabo Verde, Guiné-Bissau e S. Tomé e Príncipe (1974-2002)

The main focus of the present investigation is on the transnationalization of the education policies in Cape Verde, Guine-Bissau and San Tome and Prince from 1974 to 2002 and it deals mostly with the role played by the Portuguese co operants in this field, namely teachers, teacher trainers and education technicians. Our investigation is based mostly on the theoretical and empiric analysis of the problematic of the transnatio nalizaton of the education policies, bearing in mind the concepts formulated by several renowned authors like those by Stone(2001, 2004) as well as by Dolowitz and Marsch (2002) concerning the area of knowledge transfer. The concept transnationalization we have used throughout this dissertationshould be interpreted as a carrefour , that is, a crossroad of technical knowledge, resulting from the way the different mediators have shared their expertise and who gradually contributed to the implementation of the new education systems and the consolidation of the education policies of the countries just mentioned before. We have also analyzed specific points of reference connected both with globalization and organization sociology theories since the school is the main scope of action where the participants interact using diversified strategies due to their different interests and aims. Those schools are more and more confronted with education policies resulting from neoliberal assumptions therefore we label them terminals of the education policy journeys. The naturalist paradigm, which includes a qualitative and interpretative approach, answers for the design of this investigation, whose main strategy is the Oral History. The primary sources analyzed and the interviews made have enabled us to build our knowledge based on the grounded theory method (Glasser and Strauss, 1967), supported by the informatic programme Atlas TI. We conclude that despite the weaknesses and fragilities of the Portuguese cooperation, this is the right arena for a more convergent transference of values and education (al) systems; it is a kind of hybrid territory where the knowledge transfer suits the local reality, independently of all the dilemmas resulting from globalization.

State power and protected areas: Dynamics and contradictions of forest conservation in Madhya Pradesh, India

The traditionally coercive and state-controlled governance of protected areas for nature conservation in developing countries has in many cases undergone change in the context of widespread decentralization and liberalization. This article examines an emerging "mixed" (coercive, community- and market-oriented) conservation approach in managed-resource protected areas and its effects on state power through a case study on forest protection in the central Indian state of Madhya Pradesh. The findings suggest that imperfect decentralization and partial liberalization resulted in changed forms, rather than uniform loss, of state power. A forest co-management program paradoxically strengthened local capacity and influence of the Forest Department, which generally maintained its territorial and knowledge-based control over forests and timber management. Furthermore, deregulation and reregulation enabled the state to withdraw from uneconomic activities but also implied reduced place-based control of non-timber forest products. Generally, the new policies and programs contributed to the separation of livelihoods and forests in Madhya Pradesh. The article concludes that regulatory, community- and market-based initiatives would need to be better coordinated to lead to more effective nature conservation and positive livelihood outcomes.

One Unshakable Vision: World Class Schools for Iowa, October 3, 2011

Iowans have long shared a deep commitment to giving our children the best education possible. We recognize young people today must meet higher expectations than ever to thrive in this global, knowledge-based economy. For the sake of our children and our state, it is vitally important that we build on our tradition of excellence to improve our schools. Iowa’s house of education still has a strong foundation, but it is also in need of a major remodel to be ready for the days ahead.

Putative adverse outcome pathways relevant to neurotoxicity.

The Adverse Outcome Pathway (AOP) framework provides a template that facilitates understanding of complex biological systems and the pathways of toxicity that result in adverse outcomes (AOs). The AOP starts with an molecular initiating event (MIE) in which a chemical interacts with a biological target(s), followed by a sequential series of KEs, which are cellular, anatomical, and/or functional changes in biological processes, that ultimately result in an AO manifest in individual organisms and populations. It has been developed as a tool for a knowledge-based safety assessment that relies on understanding mechanisms of toxicity, rather than simply observing its adverse outcome. A large number of cellular and molecular processes are known to be crucial to proper development and function of the central (CNS) and peripheral nervous systems (PNS). However, there are relatively few examples of well-documented pathways that include causally linked MIEs and KEs that result in adverse outcomes in the CNS or PNS. As a first step in applying the AOP framework to adverse health outcomes associated with exposure to exogenous neurotoxic substances, the EU Reference Laboratory for Alternatives to Animal Testing (EURL ECVAM) organized a workshop (March 2013, Ispra, Italy) to identify potential AOPs relevant to neurotoxic and developmental neurotoxic outcomes. Although the AOPs outlined during the workshop are not fully described, they could serve as a basis for further, more detailed AOP development and evaluation that could be useful to support human health risk assessment in a variety of ways.

Integrating sexuality into gynaecological consultations: gynaecologists' perspectives

There are currently few studies exploring doctors' personal perspectives on integrating sexuality into medical consultations. This study focuses on the views of gynaecologists on introducing, or not introducing, sexuality into their work. A total of 30 semistructured interviews were conducted with gynaecologists in the French-speaking part of Switzerland. The thematic content analysis and computer-assisted lexical analysis (Alceste) on the interview transcripts highlighted four categories: perceptions and description of sexuality, patient's sexological history, training in sexology and perceived difficulties. It is observed that, above all, the 'medical dimension' characterises gynaecologists' perceptions. Of greater interest is our observation of disparities in gynaecologists' discussion of their practice, which is often the product of lay knowledge based on common sense and/or personal experience. Finally, the decision to integrate questions relating to sexuality seems to depend on non-medical factors such as the personal experience, interest or gender of the doctor.

The role of stereotactic ablative radiotherapy in oncological and non-oncological clinical settings: highlights from the 7th Meeting of AIRO - Young Members Working Group (AIRO Giovani).

Stereotactic ablative radiotherapy is a modern cancer treatment strategy able to deliver highly focused radiation in one or a few fractions with a radical intent in several clinical settings. Young radiation oncologists need a constant and tailored update in this context to improve patient care in daily clinical practice. A recent meeting of AIRO Giovani (AIRO - Young Members Working Group) was specifically addressed to this topic, presenting state-of-the-art knowledge, based on the latest evidence in this field. Highlights of the congress are summarized and presented in this report, including thorough contributions of the speakers dealing with the role of stereotactic ablative radiotherapy in both oncological and non-oncological diseases, divided according to anatomical and clinical scenarios: intra-cranial settings (brain malignant primary tumors, metastases, benign tumors and functional disorders) and extra-cranial indications (lung primary tumors and metastases, thoracic re-irradiation, liver, lymph node and bone metastases, prostate cancer). With literature data discussed during the congress as a background, stereotactic ablative radiotherapy has proved to be a consolidated treatment approach in specific oncological and non-oncological scenarios, as well as a promising option in other clinical settings, requiring a further prospective validation in the near future. We herein present an updated overview of stereotactic ablative radiotherapy use in the clinic.

La competència "El treball col·laboratiu": una oportunitat per a incorporar les TIC en la didàctica universitària. Descripció de l'experiència amb la plataforma ACME (UdG) = La competencia "El trabajo colaborativo": una oportunidad para incorporar las TIC en la didáctica universitaria. Descripción de la experiencia con la plataforma ACME (UdG)

L'article és una reflexió sobre els requisits de formació dels professionals que demana la societat del coneixement. Un dels objectius més importants que ha de tenir la universitat en la societat del coneixement és la formació de professionals competents que tinguin prou eines intel·lectuals per a enfrontar-se a la incertesa de la informació, a la consciència que aquesta té una data de caducitat a curt termini i a l'ansietat que això provoca. Però, a més, també han de ser capaços de definir i crear les eines de treball amb què donaran sentit i eficàcia a aquest coneixement mudable i mutant. Per això, l'espai europeu d'ensenyament superior prioritza la competència transversal del treball col·laboratiu amb l'objectiu de promoure un aprenentatge autònom, compromès i adaptat a les noves necessitats de l'empresa del segle xxi. En aquest context, es presenta l'entorn teòric que fonamenta el treball desenvolupat a la plataforma informàtica ACME, que uneix el treball col·laboratiu i l'aprenentatge semipresencial o blended learning. Així mateix, es descriuen amb detall alguns exemples de wikis, paradigma del treball col·laboratiu, fets en assignatures impartides per la Universitat de Girona en l'espai virtual ACME

La competència "El treball col·laboratiu": una oportunitat per a incorporar les TIC en la didàctica universitària. Descripció de l'experiència amb la plataforma ACME (UdG) = La competencia "El trabajo colaborativo": una oportunidad para incorporar las TIC en la didáctica universitaria. Descripción de la experiencia con la plataforma ACME (UdG)

L'article és una reflexió sobre els requisits de formació dels professionals que demana la societat del coneixement. Un dels objectius més importants que ha de tenir la universitat en la societat del coneixement és la formació de professionals competents que tinguin prou eines intel·lectuals per a enfrontar-se a la incertesa de la informació, a la consciència que aquesta té una data de caducitat a curt termini i a l'ansietat que això provoca. Però, a més, també han de ser capaços de definir i crear les eines de treball amb què donaran sentit i eficàcia a aquest coneixement mudable i mutant. Per això, l'espai europeu d'ensenyament superior prioritza la competència transversal del treball col·laboratiu amb l'objectiu de promoure un aprenentatge autònom, compromès i adaptat a les noves necessitats de l'empresa del segle xxi. En aquest context, es presenta l'entorn teòric que fonamenta el treball desenvolupat a la plataforma informàtica ACME, que uneix el treball col·laboratiu i l'aprenentatge semipresencial o blended learning. Així mateix, es descriuen amb detall alguns exemples de wikis, paradigma del treball col·laboratiu, fets en assignatures impartides per la Universitat de Girona en l'espai virtual ACME

Information and Communication Society's Impact on Global Paper Consumption

Tämän tutkielman tavoitteena on selvittää informaatio- ja kommunikaatioyhteiskunnan vaikutusta paperin kulutukseen maailmanlaajuisesti. Tarkoituksena on löytää informaatio- ja kommunikaatioyhteiskuntaa kuvaavia mittareita, joiden avulla voidaan vertailla kehittyneitä ja kehittyviä markkina-alueita keskenään. Tutkimusongelmaan haetaan ratkaisua tutkimalla sekä kirjallisuutta että tilastoja, ja vertaamalla niitä esitettyihin teorioihin informaatio- ja kommunikaatioyhteiskunnan kehityksestä. Tutkielman avulla pyritään arvioimaan ja kuvaamaantoimintaympäristön muutoksia paperin kulutuksen suhteen pitkällä aikavälillä informaatio- ja kommunikaatioyhteiskunnan näkökulmasta.

Hiljaisen tiedon tallennusHämeen Puhelin Oy:ssä vuosina 2006-2010

Moderni liiketoiminta kohtaa uusia haasteita. Haasteiden aiheuttajia ovat mm. alenevat tuotantokustannukset ja kiihtyvä kilpailu. Jotta yritys kykenisi vastaamaan näihin moderneihin haasteisiin, sen tulee toimissaan hyödyntää tehokkaasti omat resurssit. Yrityksen suurimmat resurssit sijaitsevat henkilöstössä, heihin sitoutuneessa tiedossa. Tästä tiedosta iso osa on ns. hiljaista tietoa, jota ei voida perinteisin keinoin tallentaa. Tämä työ, tutkimus keskittyy tuon hiljaisen tiedon tallentamiseen. Tutkimuksen tavoitteena oli luoda malli, joka sisältää hiljaisen tiedon keruun, analyysin ja siirtämisen. Kokonaisuus muodostaa työkalun jolla teettävän yrityksen eläkkeelle jäävä henkilöstön hiljainen tieto tallennetaan yritykseen. Mallin lisäksi tutkimuksessa tuodaan esille aihetta koskevat erilaiset kehitysmahdollisuudet ja visiot.