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.

Quality of Web-based information on obsessive compulsive disorder.

BACKGROUND: The Internet is increasingly used as a source of information for mental health issues. The burden of obsessive compulsive disorder (OCD) may lead persons with diagnosed or undiagnosed OCD, and their relatives, to search for good quality information on the Web. This study aimed to evaluate the quality of Web-based information on English-language sites dealing with OCD and to compare the quality of websites found through a general and a medically specialized search engine. METHODS: Keywords related to OCD were entered into Google and OmniMedicalSearch. Websites were assessed on the basis of accountability, interactivity, readability, and content quality. The "Health on the Net" (HON) quality label and the Brief DISCERN scale score were used as possible content quality indicators. Of the 235 links identified, 53 websites were analyzed. RESULTS: The content quality of the OCD websites examined was relatively good. The use of a specialized search engine did not offer an advantage in finding websites with better content quality. A score ≥16 on the Brief DISCERN scale is associated with better content quality. CONCLUSION: This study shows the acceptability of the content quality of OCD websites. There is no advantage in searching for information with a specialized search engine rather than a general one. Practical implications: The Internet offers a number of high quality OCD websites. It remains critical, however, to have a provider-patient talk about the information found on the Web.

Advantages of a modified gastroscope for video-assisted internal mammary artery harvesting.

Instead of standard rigid thoracoscopes, we used a modified gastroscope for video assistance during 12 minimally invasive left internal mammary harvesting. Flexibility and remote control of its last centimeters give to the gastroscope a total freedom of movements, and perfect positioning in every direction. The scope is equipped with cold light, a suction canal and an irrigation canal, which allow for in situ washing without needing to remove it from the thoracic cavity. Thanks to these advantages, vision and lighting are always perfect.

Swiss Democracy on the Web 2010 : Society and Politics in a Connected Age

The rapid adoption of online media like Facebook, Twitter or Wikileaks leaves us with little time to think. Where is information technology taking us, our society and our democratic institutions ? Is the Web replicating social divides that already exist offline or does collaborative technology pave the way for a more equal society ? How do we find the right balance between openness and privacy ? Can social media improve civic participation or do they breed superficial exchange and the promotion of false information ? These and lots of other questions arise when one starts to look at the Internet, society and politics. The first part of this paper gives an overview of the social changes that occur with the rise of the Web. The second part serves as an overview on how the Web is being used for political participation in Switzerland and abroad. Le développement rapide de nouveaux médias comme Facebook, Twitter ou Wikileaks ne laisse que peu de temps à la réflexion. Quels sont les changements que ces technologies de l'information impliquent pour nous, notre société et nos institutions démocratiques ? Internet ne fait-il que reproduire des divisions sociales qui lui préexistent ou constitue-t-il un moyen de lisser et d'égaliser ces mêmes divisions ? Comment trouver le bon équilibre entre transparence et respect de la vie privée ? Les médias sociaux permettent-ils de stimuler la participation politique ou ne sont-ils que le vecteur d'échanges superficiels et de fausses informations ? Ces questions, parmi d'autres, émergent rapidement lorsque l'on s'intéresse à la question des liens entre Internet, la société et la politique. La première partie de ce cahier est consacrée aux changements sociaux générés par l'émergence et le développement d'Internet. La seconde fait l'état des lieux de la manière dont Internet est utilisé pour stimuler la participation politique en Suisse et à l'étranger.

Frame detection over the semantic web

In the past, research in ontology learning from text has mainly focused on entity recognition, taxonomy induction and relation extraction. In this work we approach a challenging research issue: detecting semantic frames from texts and using them to encode web ontologies. We exploit a new generation Natural Language Processing technology for frame detection, and we enrich the frames acquired so far with argument restrictions provided by a super-sense tagger and domain specializations. The results are encoded according to a Linguistic MetaModel, which allows a complete translation of lexical resources and data acquired from text, enabling custom transformations of the enriched frames into modular ontology components.

The AO comprehensive classification of pediatric long-bone fractures: a web-based multicenter agreement study.

The first AO comprehensive pediatric long-bone fracture classification system has been proposed following a structured path of development and validation with experienced pediatric surgeons. A Web-based multicenter agreement study involving 70 surgeons in 15 clinics and 5 countries was conducted to assess the reliability and accuracy of this classification when used by a wide range of surgeons with various levels of experience. Training was provided at each clinic before the session. Using the Internet, participants could log in at any time and classify 275 supracondylar, radius, and tibia fractures at their own pace. The fracture diagnosis was made following the hierarchy of the classification system using both clinical terminology and codes. kappa coefficients for the single-surgeon diagnosis of epiphyseal, metaphyseal, or diaphyseal fracture type were 0.66, 0.80, and 0.91, respectively. Median accuracy estimates for each bone and type were all greater than 80%. Depending on their experience and specialization, surgeons greatly varied in their ability to classify fractures. Pediatric training and at least 2 years of experience were associated with significant improvement in reliability and accuracy. Kappa coefficients for diagnosis of specific child patterns were 0.51, 0.63, and 0.48 for epiphyseal, metaphyseal, and diaphyseal fractures, respectively. Identified reasons for coding discrepancies were related to different understandings of terminology and definitions, as well as poor quality radiographic images. Results supported some minor adjustments in the coding of fracture type and child patterns. This classification system received wide acceptance and support among the surgeons involved. As long as appropriate training could be performed, the system classification was reliable, especially among surgeons with a minimum of 2 years of clinical experience. We encourage broad-based consultation between surgeons' international societies and the use of this classification system in the context of clinical practice as well as prospectively for clinical studies.

Evaluation of an online, case-based interactive approach to teaching pathophysiology

Rapport de synthèse : L'article qui fait l'objet de ma thèse évalue une nouvelle approche pédagogique pour l'apprentissage de certains chapitres de physiopathologie. Le dispositif pédagogique se base sur l'alternance d'apprentissage ex-cathedra et de l'utilisation d'un site web comprenant des vignettes cliniques. Lors de la consultation de ces-dernières, l'étudiant est invité à demander des examens de laboratoire dont il pourrait justifier la pertinence selon le cas clinique étudié. La nouveauté du procédé réside dans le fait que, préalablement à son cours ex-cathedra, l'enseignant peut consulter les statistiques de demandes de laboratoire et ainsi orienter son cours selon les éléments mal compris par les étudiants. A la suite du cours ex-cathedra, les étudiants peuvent consulter sur internet la vignette clinique complète avec des explications. A l'issue de tout le cours, une évaluation auprès des étudiants a été conduite. Le procédé a été mis en place durant deux années consécutives et l'article en discute notamment les résultats. Nous avons pu conclure que cette méthode innovatrice d'enseignement amène les étudiants à mieux se préparer pour les cours ex-cathedra tout en permettant à l'enseignant d'identifier plus précisément quelles thématiques étaient difficiles pour les étudiants et donc d'ajuster au mieux son cours. Mon travail de thèse a consisté à créer ce dispositif d'apprentissage, à créer l'application web des vignettes cliniques et à l'implanter durant deux années consécutives. J'ai ensuite analysé les données des évaluations et écrit l'article que j'ai présenté à la revue 'Medical Teacher'. Après quelques corrections et précisions demandées par le comité de lecture, l'article a été accepté et publié. Ce travail a débouché sur une seconde version de l'application web qui est actuellement utilisée lors du module 3.1 de 3è année à l'Ecole de Médecine à Lausanne. Summary : Since the early days of sexual selection, our understanding of the selective forces acting on males and females during reproduction has increased remarkably. However, despite a long tradition of experimental and theoretical work in this field and relentless effort, numerous questions remain unanswered and many results are conflicting. Moreover, the interface between sexual selection and conservation biology has to date received little attention, despite existing evidence for its importance. In the present thesis, I first used an empirical approach to test various sexual selection hypotheses in a population of whitefish of central Switzerland. This precise population is characterized by a high prevalence of gonadal alterations in males. In particular, I challenged the hypothesis that whitefish males displaying peculiar gonadal features are of lower genetic quality than other seemingly normal males. Additionally, I also worked on identifying important determinant of sperm behavior. During a second theoretical part of my work, which is part of a larger project on the evolution of female mate preferences in harvested fish populations, I developed an individual-based simulation model to estimate how different mate discrimination costs affect the demographical behavior of fish populations and the evolutionary trajectories of female mate preferences. This latter work provided me with some insight on a recently published article addressing the importance of sexual selection for harvesting-induced evolution. I built upon this insight in a short perspective paper. In parallel, I let some methodological questions drive my thoughts, and wrote an essay about possible synergies between the biological, the philosophical and the statistical approach to biological questions.

Iliac wing fracture following graft harvesting from the anterior iliac crest: literature review based on a case report.

The morbidity of bone graft harvesting from the iliac crest has been widely discussed in the literature. For some authors, it is considered to be low and for others relatively high. We report on a case of a fracture of the iliac wing after graft harvesting from the anterior iliac crest despite good surgical technique. This complication is well known and most of these fractures heal uneventfully if treated conservatively. However, if anatomical and technical considerations are respected, the patient could be spared this inconvenience. Based on a literature review, we discuss the procedure's potential complications and how to avoid them in an update.

The International LAM Registry: a component of an innovative web-based clinician, researcher, and patient-driven rare disease research platform.

BACKGROUND: A relative inability to capture a sufficiently large patient population in any one geographic location has traditionally limited research into rare diseases. METHODS AND RESULTS: Clinicians interested in the rare disease lymphangioleiomyomatosis (LAM) have worked with the LAM Treatment Alliance, the MIT Media Lab, and Clozure Associates to cooperate in the design of a state-of-the-art data coordination platform that can be used for clinical trials and other research focused on the global LAM patient population. This platform is a component of a set of web-based resources, including a patient self-report data portal, aimed at accelerating research in rare diseases in a rigorous fashion. CONCLUSIONS: Collaboration between clinicians, researchers, advocacy groups, and patients can create essential community resource infrastructure to accelerate rare disease research. The International LAM Registry is an example of such an effort. 82.

Are the light-harvesting I complexes from Rhodospirillum rubrum arranged around the reaction centre in a square geometry?

The basic photosynthetic unit containing the reaction centre and the light-harvesting I complex (RC-LHI) of the purple non-sulphur bacterium Rhodospirillum rubrum was purified and reconstituted into two-dimensional (2D) membrane crystals. Transmission electron microscopy using conventional techniques and cryoelectron microscopy of the purified single particles and of 2D crystals yielded a projection of the RC-LHI complex at a resolution of at least 1.6 nm. In this projection the LHI ring appears to have a square symmetry and packs in a square crystal lattice. The square geometry of the LHI ring was observed also in images of single isolated particles of the RC-LHI complex. However, although the LHI units are packed identically within the crystal lattice, a new rotational analysis developed here showed that the reaction centres take up one of four possible orientations within the ring. This fourfold disorder supports our interpretation of a square ring symmetry and suggests that a hitherto undetected component may be present within the photosynthetic unit.

Medication use in pregnancy: a cross-sectional, multinational web-based study.

OBJECTIVES: Intercountry comparability between studies on medication use in pregnancy is difficult due to dissimilarities in study design and methodology. This study aimed to examine patterns and factors associated with medications use in pregnancy from a multinational perspective, with emphasis on type of medication utilised and indication for use. DESIGN: Cross-sectional, web-based study performed within the period from 1 October 2011 to 29 February 2012. Uniform collection of drug utilisation data was performed via an anonymous online questionnaire. SETTING: Multinational study in Europe (Western, Northern and Eastern), North and South America and Australia. PARTICIPANTS: Pregnant women and new mothers with children less than 1 year of age. PRIMARY AND SECONDARY OUTCOME MEASURES: Prevalence of and factors associated with medication use for acute/short-term illnesses, chronic/long-term disorders and over-the-counter (OTC) medication use. RESULTS: The study population included 9459 women, of which 81.2% reported use of at least one medication (prescribed or OTC) during pregnancy. Overall, OTC medication use occurred in 66.9% of the pregnancies, whereas 68.4% and 17% of women reported use of at least one medication for treatment of acute/short-term illnesses and chronic/long-term disorders, respectively. The extent of self-reported medicated illnesses and types of medication used by indication varied across regions, especially in relation to urinary tract infections, depression or OTC nasal sprays. Women with higher age or lower educational level, housewives or women with an unplanned pregnancy were those most often reporting use of medication for chronic/long-term disorders. Immigrant women in Western (adjusted OR (aOR): 0.55, 95% CI 0.34 to 0.87) and Northern Europe (aOR: 0.50, 95% CI 0.31 to 0.83) were less likely to report use of medication for chronic/long-term disorders during pregnancy than non-immigrants. CONCLUSIONS: In this study, the majority of women in Europe, North America, South America and Australia used at least one medication during pregnancy. There was a substantial inter-region variability in the types of medication used.