Protein homology reveals new targets for bioactive small molecules.

MOTIVATION: The functional impact of small molecules is increasingly being assessed in different eukaryotic species through large-scale phenotypic screening initiatives. Identifying the targets of these molecules is crucial to mechanistically understand their function and uncover new therapeutically relevant modes of action. However, despite extensive work carried out in model organisms and human, it is still unclear to what extent one can use information obtained in one species to make predictions in other species. RESULTS: Here, for the first time, we explore and validate at a large scale the use of protein homology relationships to predict the targets of small molecules across different species. Our results show that exploiting target homology can significantly improve the predictions, especially for molecules experimentally tested in other species. Interestingly, when considering separately orthology and paralogy relationships, we observe that mapping small molecule interactions among orthologs improves prediction accuracy, while including paralogs does not improve and even sometimes worsens the prediction accuracy. Overall, our results provide a novel approach to integrate chemical screening results across multiple species and highlight the promises and remaining challenges of using protein homology for small molecule target identification. AVAILABILITY AND IMPLEMENTATION: Homology-based predictions can be tested on our website http://www.swisstargetprediction.ch. CONTACT: david.gfeller@unil.ch or vincent.zoete@isb-sib.ch. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

ANÁLISE SENSORIAL DO SUCO INTEGRAL DE UVA ‘ISABEL’ SUBMETIDA À APLICAÇÃO DE ÁCIDO ABSCÍSICO

RESUMO O suco de uva ‘Isabel’ apresenta deficiência de cor e uma alternativa é o uso de ácido abscísico para aumentar a coloração. O objetivo deste trabalho foi avaliar a aceitação do suco integral de uva ‘Isabel’ tratada com ácido abscísico (S-ABA) em diferentes concentrações e épocas, por meio da análise sensorial, obtido em duas safras consecutivas (2011 e 2012). O delineamento experimental utilizado foi em blocos completos casualizados, com quatro repetições e cinco tratamentos: Testemunha; S-ABA 200 mg L-1aplicado sete dias após o início da maturação (DAIM); S-ABA 400 mg L-1 aplicado aos sete DAIM; S-ABA 200 mg L-1 aplicado aos sete DAIM + 200 mg L-1 aplicado aos 15 dias após a primeira aplicação (DAPA); e S-ABA 400 mg L-1 aplicado aos sete DAIM + 400 mg L-1, aplicado aos 15 DAPA. Os sucos integrais dos tratamentos foram obtidos pelo processo ‘Welch’, em panela extratora por arraste de vapor. Para a avaliação sensorial, contou-se com 70 julgadores não treinados, que avaliaram os atributos: coloração, aroma, sabor, corpo e aceitação global, empregando-se uma escala hedônica de nove pontos. Verificou-se que todos os sucos integrais de uva ‘Isabel’ tratada com S-ABA apresentaram maior aceitação pelos julgadores quanto aos atributos sensoriais avaliados, sendo a concentração de 400 mg L-1 em uma única aplicação, aos sete DAIM, suficiente para propiciar esses resultados.

Pautas hacia un modelo de aplicación web institucional universitaria. El caso de los webcom: sitios de facultades de comunicación de Iberoamérica

El diseño de un modelo de aplicación web institucional universitaria con categorías, propiedades y fases evolutivas específicas ejerció como unidad de medida para la observación de 64 sitios web de facultades de comunicación de Iberoamérica. Finalmente, 10 sitios han sido escogidos para su análisis detallado, bajo las pautas del modelo diseñado. Los resultados señalan que menos de una decena de sitios web están en condiciones de considerarse productos eficientes de comunicación y gestión.

Balanced Scorecard -mittaristo strategisena ohjaustyökaluna konserniympäristössä. Case: Stora Enso Packaging Oy

Tässä pro gradu -tutkielmassa analysoidaan neljästä eri näkökulmasta koostuvan Balanced Scorecardin soveltamista strategisena ohjaustyökaluna. Tavoitteena on Balanced Scorecardin toteuttamiseen liittyvän strategisen päätöksenteon tukeminen. Teoriaosuus on toteutettu kirjallisuuden pohjalta ja empiirinen aineisto on koottu lähinnä case-yrityksen omasta Balanced Scorecard -projektista. Case-yritys on maailmanlaajuisem Stora Enso -konsernin täysin omistama täyden palvelun aaltopahviratkaisuihin erikoistunut tytäryhtiökonserni. Balanced Scorecard -projekti yrityksessä on ollu käynnissä jo parin vuoden ajan ja nykyään käytössä on myös atk-pohjainen Balanced Scorecard -ohjelmisto. Tulevaisuudessa tavoitteena on Balanced Scorecardin ja siihen liityvän ohjelmiston ottaminen käyttöön koko konsernin kaikilla organisaatiotasoilla. Tutkimuksen tuloksena mallin todetaan teorian lisäksi myös käytännössä kokoavan hajanaiset tiedot tiiviiksi ja johdonmukaiseksi kokonaisuudeksi. Balanced Scorecardin onnistuminen riippuu paljolti työntekijöiden sitoutumisesta ja johdon halusta aikaansaada muutoksia. Oikein sovellettuna Balanced Scorecard on tehokas kommunikointiväline, joka kehittyy jatkuvasti organisaation mukana. Suurimpana ongelmana tai haasteena Suomessa nähdään mallin sisäistäminen alemmilla organisaatiotasoilla. Tutkimuksessa tarjotaan tähän ratkaisuksi uuden suomenkielisen käsitteen lanseeraamista ja parempaa tiedottamista esimerkiksi intranetin välityksellä.

Localisation of B2C Marketing Communications on the Internet. Case: New Product Launch

Tavoitteena on tutkia kuluttajille suunnatun markkinointiviestinnän lokalisointia Internetissä uuden tuotteen lanseerauksen yhteydessä. Vaikka Internet on globaali media, sen haasteena on tarjota paikallisesti kuluttajille merkityksellistä sisältöä, sekä ylläpitää yhtenäistä brandia. Tutkimus on toteutettu deskriptiivisenä tapaustutkimuksena globaalissa tietoliikenneyrityksessä, ja se perustuu haastatteluihin sekä valmiiseen aineistoon. Lyhentyneet kulutuselektroniikan elinkaaret, nopeat tuotelanseeraukset, kasvava yhteistyö ulkopuolisten kumppanien kanssa sekä markkinointiviestinnän integraation tarve aiheuttavat ajoitusongelmia lokalisointiin. Yhtenäinen web infrastruktuuri, työkalut ja globaalit prosessit mahdollistavat kustannustehokkaan lokalisoinnin business-tilanteen muuttuessa ja kultturieroista johtuen. Tässä tutkimuksessa on selvitetty neljän tekijän (ympäristö, tuote, kuluttaja, organisaatiostrategia) vaikutusta lokalisointiin. Jotta maiden parhaita menettelytapoja voidaan hyödyntää nykyistä paremmin ja välttää kultturierojen sivuuttaminen, tarvitaan sekä ’virallista’ että vapaamuotoista seurantaa. Globaalin Internet-sivuston ja lukuisten kansallisten sivustojen ylläpitäminen vaatii Internet-sivustojen fokuksen tarkkaa noudattamista, globaalia segmentointia, ja sen mukaista sisällön tarjontaa kuluttajille.

Establishing the Stages and Processes of Change for Weight Loss by Consensus of Experts

The present study aimed to establish, by a consensus of experts, the stages and processes of change for weight management in overweight and obese people. The first step involved developing two questionnaires aimed at assessing stages and processes of change for weight loss in overweight and obese people. The processes-ofchange questionnaire consisted of 12 subscales, and contained 107 items. A three-round Delphi study was carried out through a website, where participants were asked to give their opinion about the representativeness and clarity of the scale items. The stages-of-change questionnaire consisted of five items and was presented in the final round of the study. A team of 66 experts in the obesity field from 29 countries participated in the study. They were selected either because they belonged to the organizing committee of international associations related to obesity, or because of their research career. The required changes in the questionnaire were made according to the opinions of the participants. Some of these were the result of the group statistical response, whereas others were due to the suggestions made by the participants. A final version of the questionnaire consisting of 63 items was eventually obtained. The present study produced two questionnaires to assess stages and processes of change for weight management. The strength of the study lies in the consensus reached by the panel of experts in order to establish the required content of the questionnaires. The two measures provide useful tools for practitioners who wish to tailor weight-management interventions according to transtheoretical model constructs.

Addition of MR imaging features and genetic biomarkers strengthens glioblastoma survival prediction in TCGA patients.

PURPOSE: The purpose of our study was to assess whether a model combining clinical factors, MR imaging features, and genomics would better predict overall survival of patients with glioblastoma (GBM) than either individual data type. METHODS: The study was conducted leveraging The Cancer Genome Atlas (TCGA) effort supported by the National Institutes of Health. Six neuroradiologists reviewed MRI images from The Cancer Imaging Archive (http://cancerimagingarchive.net) of 102 GBM patients using the VASARI scoring system. The patients' clinical and genetic data were obtained from the TCGA website (http://www.cancergenome.nih.gov/). Patient outcome was measured in terms of overall survival time. The association between different categories of biomarkers and survival was evaluated using Cox analysis. RESULTS: The features that were significantly associated with survival were: (1) clinical factors: chemotherapy; (2) imaging: proportion of tumor contrast enhancement on MRI; and (3) genomics: HRAS copy number variation. The combination of these three biomarkers resulted in an incremental increase in the strength of prediction of survival, with the model that included clinical, imaging, and genetic variables having the highest predictive accuracy (area under the curve 0.679±0.068, Akaike's information criterion 566.7, P<0.001). CONCLUSION: A combination of clinical factors, imaging features, and HRAS copy number variation best predicts survival of patients with GBM.

EsPal: One-stop shopping for Spanish word properties

This article introduces EsPal: a Web-accessible repository containing a comprehensive set of properties of Spanish words. EsPal is based on an extensible set of data sources, beginning with a 300 million token written database and a 460 million token subtitle database. Properties available include word frequency, orthographic structure and neighborhoods, phonological structure and neighborhoods, and subjective ratings such as imageability. Subword structure properties are also available in terms of bigrams and trigrams, bi-phones, and bi-syllables. Lemma and part-of-speech information and their corresponding frequencies are also indexed. The website enables users to either upload a set of words to receive their properties, or to receive a set of words matching constraints on the properties. The properties themselves are easily extensible and will be added over time as they become available. It is freely available from the following website: http://www.bcbl.eu/databases/espal

Publication trends of shared decision making in 15 high impact medical journals: a full-text review with bibliometric analysis.

BACKGROUND: Shared Decision Making (SDM) is increasingly advocated as a model for medical decision making. However, there is still low use of SDM in clinical practice. High impact factor journals might represent an efficient way for its dissemination. We aimed to identify and characterize publication trends of SDM in 15 high impact medical journals. METHODS: We selected the 15 general and internal medicine journals with the highest impact factor publishing original articles, letters and editorials. We retrieved publications from 1996 to 2011 through the full-text search function on each journal website and abstracted bibliometric data. We included publications of any type containing the phrase "shared decision making" or five other variants in their abstract or full text. These were referred to as SDM publications. A polynomial Poisson regression model with logarithmic link function was used to assess the evolution across the period of the number of SDM publications according to publication characteristics. RESULTS: We identified 1285 SDM publications out of 229,179 publications in 15 journals from 1996 to 2011. The absolute number of SDM publications by journal ranged from 2 to 273 over 16 years. SDM publications increased both in absolute and relative numbers per year, from 46 (0.32% relative to all publications from the 15 journals) in 1996 to 165 (1.17%) in 2011. This growth was exponential (P < 0.01). We found fewer research publications (465, 36.2% of all SDM publications) than non-research publications, which included non-systematic reviews, letters, and editorials. The increase of research publications across time was linear. Full-text search retrieved ten times more SDM publications than a similar PubMed search (1285 vs. 119 respectively). CONCLUSION: This review in full-text showed that SDM publications increased exponentially in major medical journals from 1996 to 2011. This growth might reflect an increased dissemination of the SDM concept to the medical community.

The REporting of studies Conducted using Observational Routinely-collected health Data (RECORD) statement.

Routinely collected health data, obtained for administrative and clinical purposes without specific a priori research goals, are increasingly used for research. The rapid evolution and availability of these data have revealed issues not addressed by existing reporting guidelines, such as Strengthening the Reporting of Observational Studies in Epidemiology (STROBE). The REporting of studies Conducted using Observational Routinely collected health Data (RECORD) statement was created to fill these gaps. RECORD was created as an extension to the STROBE statement to address reporting items specific to observational studies using routinely collected health data. RECORD consists of a checklist of 13 items related to the title, abstract, introduction, methods, results, and discussion section of articles, and other information required for inclusion in such research reports. This document contains the checklist and explanatory and elaboration information to enhance the use of the checklist. Examples of good reporting for each RECORD checklist item are also included herein. This document, as well as the accompanying website and message board (http://www.record-statement.org), will enhance the implementation and understanding of RECORD. Through implementation of RECORD, authors, journals editors, and peer reviewers can encourage transparency of research reporting.

Guideline adaptation: a methodology to enhance efficiency in guideline development and improve utilization.

BACKGROUND: Developing and updating high-quality guidelines requires substantial time and resources. To reduce duplication of effort and enhance efficiency, we developed a process for guideline adaptation and assessed initial perceptions of its feasibility and usefulness. METHODS: Based on preliminary developments and empirical studies, a series of meetings with guideline experts were organised to define a process for guideline adaptation (ADAPTE) and to develop a manual and a toolkit made available on a website (http://www.adapte.org). Potential users, guideline developers and implementers, were invited to register and to complete a questionnaire evaluating their perception about the proposed process.

Kuluttajien suhtautuminen aikakauslehden brändiin ja brändin persoonallisuuteen

Pro gradun tarkoituksena oli tutkia kuluttajien suhtautumista kolmen kuluttajille suunnatun aikakauslehden brändiin ja brändin persoonallisuuteen. Tutkimuksen kohteena olevat aikakauslehdet olivat naisille suunnattu, nuorille suunnattu sekä tekniikkaan keskittynyt aikakauslehti. Tässä tutkimuksessa käytettiin kvalitatiivista tutkimusmenetelmää. Sisällön erittelyn avulla tutkittiin eroja kuluttajien suhtautumisessa eri aikakauslehtibrändien ollessa kyseessä. Kuluttajien mielipiteitä aikakauslehtibrändin persoonallisuudesta selvitettiin aikakauslehtien verkkosivuilla olleen kyselytutkimuksen avulla, jonka tuloksia analysoitiin korrespondenssianalyysissä. Korrespondenssianalyysissä kvantifioitiin kvalitatiivista aineistoa. Aikakauslehtikustantajien mielipiteitä aikakauslehden brändistä tutkittiin aikakauslehtien verkkosivujen sisällön kautta. Kuluttajat näkivät aikakausilehtien brändeissä eri persoonallisuuksien piirteitä. Syyt kuluttajien suhtautumisessa eri aikakauslehtibrändeihin johtuvat pikemminkin eri kohderyhmistä kuin kustantajan rakentamista eroista. Kustantajien ja kuluttajien mielipiteet brändin persoonallisuudesta olivat naisille suunnatussa lehdessä hyvin yhtenevät, kun taas tekniikkaan suuntautunut lehti kärsi epäselvästä brändistä.

Die Konstruktion einer medizinischen Disziplin und ihre Herausforderungen: die Orthopädie in der Schweiz im 19. und 20. Jahrhundert [The construction of a medical discipline and its challenges: Orthopedics in Switzerland during the 19th and 20th centuries].

(ENGLISH VERSION BELOW) Dieser Beitrag fügt sich in eine post-doktorale Forschung über die Geschichte der Orthopädie ein, die unter dem Mandat des Centre Hospitalier Universitaire Vaudois (CHUV) geleitet wird und teilerweise auf die Archiv der Schweizerischen Gesellschaft für Orthopädie (aktuelle Swiss Orthopaedics) beruht. Die Autorin untersucht die Herausforderungen, welche die Geschichte der Orthopädie in der Schweiz prägten und berücksichtigt dabei die Anpassungsstrategien einer medizinischen und technischen Disziplin in einer sich wandelnden Gesellschaft. Zusammenfassung der Beitrag und Informationen auf der Website der Zeitschrift: http://econtent.hogrefe.com/toc/tum/72/7 This article is inspired by a post-doctorale research about the history of orthopedics, mandated by the Centre Hospitalier Universitaire Vaudois (CHUV), and partly supported by the Archiv of the Swiss Society of Orthopedics (nowadays Swiss Orthopaedics). By examining the implications that have shaped the history of orthopedics in Switzerland, the author seeks to shed light on the strategies that were implemented in adopting a medical and technical discipline within a transforming society. Summary of the article and information on the journal's website: http://econtent.hogrefe.com/toc/tum/72/7

Educational resources offered by the European Board of Physical and Rehabilitation Medicine (EBPRM)

Background .- Physical and Rehabilitation Medicine (PRM) is a very demanding medical speciality. To ensure high standard of research and care in PRM all across Europe, it is crucial to attract gifted trainees and offer them high quality education. At undergraduate level, many medical schools in Europe omit to offer teaching on disabled persons and on basic PRM knowledge. Thus PRM is hardly known to medical students. For postgraduate trainees access to evidence-based knowledge as well as teaching of research methodology specific to PRM, rehabilitation methodology, disability management and team building also need to be strengthened to increase the visibility of PRM. Action .- To address these issues the EBPRM proposes presently a specific undergraduate curriculum in PRM including the issues of disability, participation and handicap as a basis for general medical practice and postgraduate rehabilitation training. For PRM trainees many educational documents are now available on the EBPRM website. A growing number of educational sessions for PRM trainees take place during international and national PRM Congresses which can be accessed at low cost. Educational papers published regularly in European rehabilitation journals and European PRM Schools are offered free or at very low cost to trainees.

Identification of imaging selection patterns in acute ischemic stroke patients and the influence on treatment and clinical trial enrollment decision making.

BACKGROUND AND PURPOSE: For the STroke Imaging Research (STIR) and VISTA-Imaging Investigators The purpose of this study was to collect precise information on the typical imaging decisions given specific clinical acute stroke scenarios. Stroke centers worldwide were surveyed regarding typical imaging used to work up representative acute stroke patients, make treatment decisions, and willingness to enroll in clinical trials. METHODS: STroke Imaging Research and Virtual International Stroke Trials Archive-Imaging circulated an online survey of clinical case vignettes through its website, the websites of national professional societies from multiple countries as well as through email distribution lists from STroke Imaging Research and participating societies. Survey responders were asked to select the typical imaging work-up for each clinical vignette presented. Actual images were not presented to the survey responders. Instead, the survey then displayed several types of imaging findings offered by the imaging strategy, and the responders selected the appropriate therapy and whether to enroll into a clinical trial considering time from onset, clinical presentation, and imaging findings. A follow-up survey focusing on 6 h from onset was conducted after the release of the positive endovascular trials. RESULTS: We received 548 responses from 35 countries including 282 individual centers; 78% of the centers originating from Australia, Brazil, France, Germany, Spain, United Kingdom, and United States. The specific onset windows presented influenced the type of imaging work-up selected more than the clinical scenario. Magnetic Resonance Imaging usage (27-28%) was substantial, in particular for wake-up stroke. Following the release of the positive trials, selection of perfusion imaging significantly increased for imaging strategy. CONCLUSIONS: Usage of vascular or perfusion imaging by Computed Tomography or Magnetic Resonance Imaging beyond just parenchymal imaging was the primary work-up (62-87%) across all clinical vignettes and time windows. Perfusion imaging with Computed Tomography or Magnetic Resonance Imaging was associated with increased probability of enrollment into clinical trials for 0-3 h. Following the release of the positive endovascular trials, selection of endovascular only treatment for 6 h increased across all clinical vignettes.