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.

Functional connectivity in BOLD and CBF data: similarity and reliability of resting brain networks

Resting-state functional connectivity (FC) fMRI (rs-fcMRI) offers an appealing approach to mapping the brain's intrinsic functional organization. Blood oxygen level dependent (BOLD) and arterial spin labeling (ASL) are the two main rs-fcMRI approaches to assess alterations in brain networks associated with individual differences, behavior and psychopathology. While the BOLD signal is stronger with a higher temporal resolution, ASL provides quantitative, direct measures of the physiology and metabolism of specific networks. This study systematically investigated the similarity and reliability of resting brain networks (RBNs) in BOLD and ASL. A 2×2×2 factorial design was employed where each subject underwent repeated BOLD and ASL rs-fcMRI scans on two occasions on two MRI scanners respectively. Both independent and joint FC analyses revealed common RBNs in ASL and BOLD rs-fcMRI with a moderate to high level of spatial overlap, verified by Dice Similarity Coefficients. Test-retest analyses indicated more reliable spatial network patterns in BOLD (average modal Intraclass Correlation Coefficients: 0.905±0.033 between-sessions; 0.885±0.052 between-scanners) than ASL (0.545±0.048; 0.575±0.059). Nevertheless, ASL provided highly reproducible (0.955±0.021; 0.970±0.011) network-specific CBF measurements. Moreover, we observed positive correlations between regional CBF and FC in core areas of all RBNs indicating a relationship between network connectivity and its baseline metabolism. Taken together, the combination of ASL and BOLD rs-fcMRI provides a powerful tool for characterizing the spatiotemporal and quantitative properties of RBNs. These findings pave the way for future BOLD and ASL rs-fcMRI studies in clinical populations that are carried out across time and scanners.

Technical complications and failures of zirconia-based prostheses supported by implants followed up to 7 years: a case series.

PURPOSE To evaluate technical complications and failures of zirconia-based fixed prostheses supported by implants. MATERIALS AND METHODS Consecutive patients received zirconia-based single crowns (SCs) and fixed dental prostheses (FDPs) on implants in a private clinical setting between 2005 and 2010. One dentist performed all surgical and prosthetic procedures, and one master technician performed and coordinated all laboratory procedures. One-piece computer-aided design/ computer-assisted manufacture technology was used to fabricate abutments and frameworks, which were directly connected at the implant level, where possible. All patients were involved in a recall maintenance program and were finally reviewed in 2012. Data on framework fractures, chipping of veneering ceramics, and other technical complications were recorded. The primary endpoint was failure of the prostheses, ie, the need for a complete remake. A life table analysis was calculated. RESULTS A total of 289 implants supported 193 zirconia-based prostheses (120 SCs and 73 FDPs) in 127 patients (51 men, 76 women; average age: 62.5 ± 13.4 years) who were reviewed in 2012. Twenty-five (13%) prostheses were cemented on 44 zirconia abutments and 168 (87%) prostheses were screw-retained directly at the implant level. Fracture of 3 frameworks (1 SC, 2 FDPs) was recorded, and significant chipping resulted in the remake of 3 prostheses (1 SC, 2 FDPs). The 7-year cumulative survival rate was 96.4% ± 1.99%. Minor complications comprised 5 loose screws (these were retightened), small chips associated with 3 prostheses (these were polished), and dislodgement of 3 prostheses (these were recemented). Overall, 176 prostheses remained free of technical problems. CONCLUSIONS Zirconia-based prostheses screwed directly to implants are clinically successful in the short and medium term.

The brain’s default state interacts with working memory processes in a complex and load-dependent manner

Recently, many studies about a network active during rest and deactivated during tasks emerged in the literature: the default mode network (DMN). Spatial and temporal DMN features are important markers for psychiatric diseases. Another prominent indicator of cognitive functioning, yielding information about the mental condition in health and disease, is working memory (WM) processing. In EEG studies, frontal-midline theta power has been shown to increase with load during WM retention in healthy subjects. From these findings, the conclusion can be drawn that an increase in resting state DMN activity may go along with an increase in theta power in high-load WM conditions. We followed this hypothesis in a study on 17 healthy subjects performing a visual Sternberg WM task. The DMN was obtained by a BOLD-ICA approach and its dynamics represented by the percent-strength during pre-stimulus periods. DMN dynamics were temporally correlated with EEG theta spectral power from retention intervals. This so-called covariance mapping yielded the spatial distribution of the theta EEG fluctuations associated with the dynamics of the DMN. In line with previous findings, theta power was increased at frontal-midline electrodes in high- versus low-load conditions during early WM retention. However, load-dependent correlations of DMN with theta power resulted in primarily positive correlations in low-load conditions, while during high-load conditions negative correlations of DMN activity and theta power were observed at frontal-midline electrodes. This DMN-dependent load effect reached significance during later retention. Our results show a complex and load-dependent interaction of pre-stimulus DMN activity and theta power during retention, varying over the course of the retention period. Since both, WM performance and DMN activity, are markers of mental health, our results could be important for further investigations of psychiatric populations.

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.

Land acquisition, investment, and development in the Lao coffee sector: Successes and failures

Despite the increasing acknowledgment of scholars and practitioners that many large-scale agricultural land acquisitions in developing countries fail or never materialize, empirical evidence about how and why they fail to date is still scarce. Too often, land deals are portrayed as straightforward investments and their success is taken for granted. Looking at the coffee sector in Laos, the authors of this article explore dimensions of the land grab debate that have not yet been sufficiently examined. Coffee concessionaires in southern Laos often fail to use all of the land granted them and fail to produce high yields on the land they do use. Thus, the authors challenge the often-assumed superiority and effectiveness of large-scale versus small-scale production, specifically the argument that they modernize agricultural production and optimize land use. They argue that examining failed investments is as important as studying successful ones for understanding the implications of the land grabbing phenomenon for social, economic, and environmental outcomes. Knowledge about the scale of “failed land deals” provides important motivation for national governments to close the gap between intentions and actual outcomes. This article engages with the current debate on quality of investment and challenges the approach of employing land concessions as a vehicle for economic development in the Lao coffee sector and in other sectors and countries.

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.

Zirconia-Based Screw-Retained Prostheses Supported by Implants: A Retrospective Study on Technical Complications and Failures

BACKGROUND Little information is yet available on zirconia-based prostheses supported by implants. PURPOSE To evaluate technical problems and failures of implant-supported zirconia-based prostheses with exclusive screw-retention. MATERIAL AND METHODS Consecutive patients received screw-retained zirconia-based prostheses supported by implants and were followed over a time period of 5 years. The implant placement and prosthetic rehabilitation were performed in one clinical setting, and all patients participated in the maintenance program. The treatment comprised single crowns (SCs) and fixed dental prostheses (FDPs) of three to 12 units. Screw-retention of the CAD/CAM-fabricated SCs and FDPs was performed with direct connection at the implant level. The primary outcome was the complete failure of zirconia-based prostheses; outcome measures were fracture of the framework or extensive chipping resulting in the need for refabrication. A life table analysis was performed, the cumulative survival rate (CSR) calculated, and a Kaplan-Meier curve drawn. RESULTS Two hundred and ninety-four implants supported 156 zirconia-based prostheses in 95 patients (52 men, 43 women, average age 59.1 ± 11.7 years). Sixty-five SCs and 91 FDPs were identified, comprising a total of 441 units. Fractures of the zirconia framework and extensive chipping resulted in refabrication of nine prostheses. Nearly all the prostheses (94.2%) remained in situ during the observation period. The 5-year CSR was 90.5%, and 41 prostheses (14 SCs, 27 FDPs) comprising 113 units survived for an observation time of more than 5 years. Six SCs exhibited screw loosening, and polishing of minor chipping was required for five prostheses. CONCLUSIONS This study shows that zirconia-based implant-supported fixed prostheses exhibit satisfactory treatment outcomes and that screw-retention directly at the implant level is feasible.

Implant therapy in a surgical specialty clinic: an analysis of patients, indications, surgical procedures, risk factors, and early failures

PURPOSE The aim of this study was to analyze the patient pool referred to a specialty clinic for implant surgery over a 3-year period. MATERIALS AND METHODS All patients receiving dental implants between 2008 and 2010 at the Department of Oral Surgery and Stomatology were included in the study. As primary outcome parameters, the patients were analyzed according to the following criteria: age, sex, systemic diseases, and indication for therapy. For the inserted implants, the type of surgical procedure, the types of implants placed, postsurgical complications, and early failures were recorded. A logistic regression analysis was performed to identify possible local and systemic risk factors for complications. As a secondary outcome, data regarding demographics and surgical procedures were compared with the findings of a historic study group (2002 to 2004). RESULTS A total of 1,568 patients (792 women and 776 men; mean age, 52.6 years) received 2,279 implants. The most frequent indication was a single-tooth gap (52.8%). Augmentative procedures were performed in 60% of the cases. Tissue-level implants (72.1%) were more frequently used than bone-level implants (27.9%). Regarding dimensions of the implants, a diameter of 4.1 mm (59.7%) and a length of 10 mm (55.0%) were most often utilized. An early failure rate of 0.6% was recorded (13 implants). Patients were older and received more implants in the maxilla, and the complexity of surgical interventions had increased when compared to the patient pool of 2002 to 2004. CONCLUSION Implant therapy performed in a surgical specialty clinic utilizing strict patient selection and evidence-based surgical protocols showed a very low early failure rate of 0.6%.

Identification of Interactions in the NMD Complex Using Proximity-Dependent Biotinylation (BioID)

Proximity-dependent trans-biotinylation by the Escherichia coli biotin ligase BirA mutant R118G (BirA*) allows stringent streptavidin affinity purification of proximal proteins. This so-called BioID method provides an alternative to the widely used co-immunoprecipitation (co-IP) to identify protein-protein interactions. Here, we used BioID, on its own and combined with co-IP, to identify proteins involved in nonsense-mediated mRNA decay (NMD), a post-transcriptional mRNA turnover pathway that targets mRNAs that fail to terminate translation properly. In particular, we expressed BirA* fused to the well characterized NMD factors UPF1, UPF2 and SMG5 and detected by liquid chromatography-coupled tandem mass spectrometry (LC-MS/MS) the streptavidin-purified biotinylated proteins. While the identified already known interactors confirmed the usefulness of BioID, we also found new potentially important interactors that have escaped previous detection by co-IP, presumably because they associate only weakly and/or very transiently with the NMD machinery. Our results suggest that SMG5 only transiently contacts the UPF1-UPF2-UPF3 complex and that it provides a physical link to the decapping complex. In addition, BioID revealed among others CRKL and EIF4A2 as putative novel transient interactors with NMD factors, but whether or not they have a function in NMD remains to be elucidated.

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.