Combining Bottom-up and Top-down Generation of Interactive Knowledge Maps for Enterprise Search

Our research project develops an intranet search engine with concept- browsing functionality, where the user is able to navigate the conceptual level in an interactive, automatically generated knowledge map. This knowledge map visualizes tacit, implicit knowledge, extracted from the intranet, as a network of semantic concepts. Inductive and deductive methods are combined; a text ana- lytics engine extracts knowledge structures from data inductively, and the en- terprise ontology provides a backbone structure to the process deductively. In addition to performing conventional keyword search, the user can browse the semantic network of concepts and associations to find documents and data rec- ords. Also, the user can expand and edit the knowledge network directly. As a vision, we propose a knowledge-management system that provides concept- browsing, based on a knowledge warehouse layer on top of a heterogeneous knowledge base with various systems interfaces. Such a concept browser will empower knowledge workers to interact with knowledge structures.

Interactive Segmentation of MR Images from Brain Tumor Patients

Medical doctors often do not trust the result of fully automatic segmentations because they have no possibility to make corrections if necessary. On the other hand, manual corrections can introduce a user bias. In this work, we propose to integrate the possibility for quick manual corrections into a fully automatic segmentation method for brain tumor images. This allows for necessary corrections while maintaining a high objectiveness. The underlying idea is similar to the well-known Grab-Cut algorithm, but here we combine decision forest classification with conditional random field regularization for interactive segmentation of 3D medical images. The approach has been evaluated by two different users on the BraTS2012 dataset. Accuracy and robustness improved compared to a fully automatic method and our interactive approach was ranked among the top performing methods. Time for computation including manual interaction was less than 10 minutes per patient, which makes it attractive for clinical use.

Interactive Diffraction from Biological Nanostructures

We describe a technique for interactive rendering of diffraction effects produced by biological nanostructures, such as snake skin surface gratings. Our approach uses imagery from atomic force microscopy that accurately captures the geometry of the nanostructures responsible for structural colouration, that is, colouration due to wave interference, in a variety of animals. We develop a rendering technique that constructs bidirectional reflection distribution functions (BRDFs) directly from the measured data and leverages pre-computation to achieve interactive performance. We demonstrate results of our approach using various shapes of the surface grating nanostructures. Finally, we evaluate the accuracy of our pre-computation-based technique and compare to a reference BRDF construction technique.

FAIR_OSCE – Feedback structure for assessment of interactive roleplay in Objective Structured Clinical Exams

Introduction Since the quality of patient portrayal of standardized patients (SPs) during an Objective Structured Clinical Exam (OSCE) has a major impact on the reliability and validity of the exam, quality control should be initiated. Literature about quality control of SPs’ performance focuses on feedback [1, 2] or completion of checklists [3, 4]. Since we did not find a published instrument meeting our needs for the assessment of patient portrayal, we developed such an instrument after being inspired by others [5] and used it in our high-stakes exam. Project description SP trainers from five medical faculties collected and prioritized quality criteria for patient portrayal. Items were revised twice, based on experiences during OSCEs. The final instrument contains 14 criteria for acting (i.e. adequate verbal and non-verbal expression) and standardization (i.e. verbatim delivery of the first sentence). All partners used the instrument during a high-stakes OSCE. SPs and trainers were introduced to the instrument. The tool was used in training (more than 100 observations) and during the exam (more than 250 observations). Outcome High quality of SPs’ patient portrayal during the exam was documented. More than 90% of SP performances were rated to be completely correct or sufficient. An increase in quality of performance between training and exam was noted. For example, the rate of completely correct reaction in medical tests increased from 88% to 95%. Together with 4% of sufficient performances these 95% add up to 99% of the reactions in medical tests meeting the standards of the exam. SP educators using the instrument reported an augmentation of SPs’ performance induced by the use of the instrument. Disadvantages mentioned were the high concentration needed to observe all criteria and the cumbersome handling of the paper-based forms. Discussion We were able to document a very high quality of SP performance in our exam. The data also indicates that our training is effective. We believe that the high concentration needed using the instrument is well invested, considering the observed enhancement of performance. The development of an iPad-based application for the form is planned to address the cumbersome handling of the paper.

PDB-Explorer: a web-based interactive map of the protein data bank in shape space

Background The RCSB Protein Data Bank (PDB) provides public access to experimentally determined 3D-structures of biological macromolecules (proteins, peptides and nucleic acids). While various tools are available to explore the PDB, options to access the global structural diversity of the entire PDB and to perceive relationships between PDB structures remain very limited. Methods A 136-dimensional atom pair 3D-fingerprint for proteins (3DP) counting categorized atom pairs at increasing through-space distances was designed to represent the molecular shape of PDB-entries. Nearest neighbor searches examples were reported exemplifying the ability of 3DP-similarity to identify closely related biomolecules from small peptides to enzyme and large multiprotein complexes such as virus particles. The principle component analysis was used to obtain the visualization of PDB in 3DP-space. Results The 3DP property space groups proteins and protein assemblies according to their 3D-shape similarity, yet shows exquisite ability to distinguish between closely related structures. An interactive website called PDB-Explorer is presented featuring a color-coded interactive map of PDB in 3DP-space. Each pixel of the map contains one or more PDB-entries which are directly visualized as ribbon diagrams when the pixel is selected. The PDB-Explorer website allows performing 3DP-nearest neighbor searches of any PDB-entry or of any structure uploaded as protein-type PDB file. All functionalities on the website are implemented in JavaScript in a platform-independent manner and draw data from a server that is updated daily with the latest PDB additions, ensuring complete and up-to-date coverage. The essentially instantaneous 3DP-similarity search with the PDB-Explorer provides results comparable to those of much slower 3D-alignment algorithms, and automatically clusters proteins from the same superfamilies in tight groups. Conclusion A chemical space classification of PDB based on molecular shape was obtained using a new atom-pair 3D-fingerprint for proteins and implemented in a web-based database exploration tool comprising an interactive color-coded map of the PDB chemical space and a nearest neighbor search tool. The PDB-Explorer website is freely available at www.​cheminfo.​org/​pdbexplorer and represents an unprecedented opportunity to interactively visualize and explore the structural diversity of the PDB.

Similarity Mapplet: Interactive Visualization of the Directory of Useful Decoys and ChEMBL in High Dimensional Chemical Spaces

An Internet portal accessible at www.gdb.unibe.ch has been set up to automatically generate color-coded similarity maps of the ChEMBL database in relation to up to two sets of active compounds taken from the enhanced Directory of Useful Decoys (eDUD), a random set of molecules, or up to two sets of user-defined reference molecules. These maps visualize the relationships between the selected compounds and ChEMBL in six different high dimensional chemical spaces, namely MQN (42-D molecular quantum numbers), SMIfp (34-D SMILES fingerprint), APfp (20-D shape fingerprint), Xfp (55-D pharmacophore fingerprint), Sfp (1024-bit substructure fingerprint), and ECfp4 (1024-bit extended connectivity fingerprint). The maps are supplied in form of Java based desktop applications called “similarity mapplets” allowing interactive content browsing and linked to a “Multifingerprint Browser for ChEMBL” (also accessible directly at www.gdb.unibe.ch) to perform nearest neighbor searches. One can obtain six similarity mapplets of ChEMBL relative to random reference compounds, 606 similarity mapplets relative to single eDUD active sets, 30 300 similarity mapplets relative to pairs of eDUD active sets, and any number of similarity mapplets relative to user-defined reference sets to help visualize the structural diversity of compound series in drug optimization projects and their relationship to other known bioactive compounds.

Italo-Swiss "Chalk and blackboard interactive 2-day workshop"-participants feedback

Ten "chalk and blackboard interactive workshops" have taken place between 2011 and 2015 in Southern Switzerland or Italy. Students, residents and expert pediatricians meet during 2 days and discuss 10-15 cases. Pediatricians promote reasoning, provide supporting information and correct statements. Emphasis is placed on history taking and examination, and on all participants being involved in a stimulating atmosphere. Thirty-seven participants were asked, ≥3 months after workshop-completion, to evaluate the workshop and a recent teaching session. Thirty answered and scored the workshop as excellent (N = 24) or above average (N = 6). The scores assigned to the workshop were higher (P < 0.001) than those assigned to the lecture-based teaching.

Timely Reporting and Interactive Visualization of Animal Health and Slaughterhouse Surveillance Data in Switzerland

The reporting of outputs from health surveillance systems should be done in a near real-time and interactive manner in order to provide decision makers with powerful means to identify, assess, and manage health hazards as early and efficiently as possible. While this is currently rarely the case in veterinary public health surveillance, reporting tools do exist for the visual exploration and interactive interrogation of health data. In this work, we used tools freely available from the Google Maps and Charts library to develop a web application reporting health-related data derived from slaughterhouse surveillance and from a newly established web-based equine surveillance system in Switzerland. Both sets of tools allowed entry-level usage without or with minimal programing skills while being flexible enough to cater for more complex scenarios for users with greater programing skills. In particular, interfaces linking statistical softwares and Google tools provide additional analytical functionality (such as algorithms for the detection of unusually high case occurrences) for inclusion in the reporting process. We show that such powerful approaches could improve timely dissemination and communication of technical information to decision makers and other stakeholders and could foster the early-warning capacity of animal health surveillance systems.

RNA-Guided Genome Editing

Ciliates have evolved highly complex and intricately controlled pathways to ensure the precise and complete removal of all genomic sequences not required for vegetative growth. At the same time, they retain a reference copy of all their genetic information for future generations. This chapter describes how different ciliates use RNA-mediated DNA comparison processes to form new somatic nuclei from germline nuclei. While these processes vary in their precise mechanisms, they all use RNA to target genomic DNA sequences—either for retention or elimination. They also all consist of more than one individual pathway acting cooperatively—the two subsets of small RNAs in Paramecium and the guide RNAs and Piwi-interacting RNAs in Oxytricha—to ensure a strong belt-and-braces approach to consistent and precise somatic nucleus development. Nonetheless, this genome comparison approach to somatic nucleus development provides an elegant method for trans-generational environmental adaptation. Conceptually, it is easy to imagine how somatic changes that occur during vegetative growth could be transferred to meiotic offspring, while an unaltered germline genome is retained. Further research in this area will have far-reaching implications for the trans-generational adaptation of more distantly related eukaryotes, such as humans.