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.

Improving Pediatric Basic Life Support Performance Through Blended Learning With Web-Based Virtual Patients: Randomized Controlled Trial

BACKGROUND E-learning and blended learning approaches gain more and more popularity in emergency medicine curricula. So far, little data is available on the impact of such approaches on procedural learning and skill acquisition and their comparison with traditional approaches. OBJECTIVE This study investigated the impact of a blended learning approach, including Web-based virtual patients (VPs) and standard pediatric basic life support (PBLS) training, on procedural knowledge, objective performance, and self-assessment. METHODS A total of 57 medical students were randomly assigned to an intervention group (n=30) and a control group (n=27). Both groups received paper handouts in preparation of simulation-based PBLS training. The intervention group additionally completed two Web-based VPs with embedded video clips. Measurements were taken at randomization (t0), after the preparation period (t1), and after hands-on training (t2). Clinical decision-making skills and procedural knowledge were assessed at t0 and t1. PBLS performance was scored regarding adherence to the correct algorithm, conformance to temporal demands, and the quality of procedural steps at t1 and t2. Participants' self-assessments were recorded in all three measurements. RESULTS Procedural knowledge of the intervention group was significantly superior to that of the control group at t1. At t2, the intervention group showed significantly better adherence to the algorithm and temporal demands, and better procedural quality of PBLS in objective measures than did the control group. These aspects differed between the groups even at t1 (after VPs, prior to practical training). Self-assessments differed significantly only at t1 in favor of the intervention group. CONCLUSIONS Training with VPs combined with hands-on training improves PBLS performance as judged by objective measures.

The multiple location time weighted index: Using patient activity spaces to calculate primary care service areas

Geographic health planning analyses, such as service area calculations, are hampered by a lack of patient-specific geographic data. Using the limited patient address information in patient management systems, planners analyze patient origin based on home address. But activity space research done sparingly in public health and extensively in non-health related arenas uses multiple addresses per person when analyzing accessibility. Also, health care access research has shown that there are many non-geographic factors that influence choice of provider. Most planning methods, however, overlook non-geographic factors influencing choice of provider, and the limited data mean the analyses can only be related to home address. This research attempted to determine to what extent geography plays a part in patient choice of provider and to determine if activity space data can be used to calculate service areas for primary care providers. ^ During Spring 2008, a convenience sample of 384 patients of a locally-funded Community Health Center in Houston, Texas, completed a survey that asked about what factors are important when he or she selects a health care provider. A subset of this group (336) also completed an activity space log that captured location and time data on the places where the patient regularly goes. ^ Survey results indicate that for this patient population, geography plays a role in their choice of health care provider, but it is not the most important reason for choosing a provider. Other factors for choosing a health care provider such as the provider offering "free or low cost visits", meeting "all of the patient's health care needs", and seeing "the patient quickly" were all ranked higher than geographic reasons. ^ Analysis of the patient activity locations shows that activity spaces can be used to create service areas for a single primary care provider. Weighted activity-space-based service areas have the potential to include more patients in the service area since more than one location per patient is used. Further analysis of the logs shows that a reduced set of locations by time and type could be used for this methodology, facilitating ongoing data collection for activity-space-based planning efforts. ^

Evaluation of a Blended Refuge for Corn Rootworm

The purpose of this study was to evaluate the effectiveness of the blended refuge concept against corn rootworms. The treatments evaluated include a pure stand of Herculex XTRA (HXX), a pure stand of Roundup Ready 2 (RR2), a pure stand of RR2 with Force 3G applied overtop, and two treatments with the refuge in a bag concept–one with 95 percent HXX and a 5 percent RR2 blended refuge and the other with 90 percent HXX and a 10 percent RR2 blended refuge.

Analytic Kramer kernels, Lagrange-type interpolation series and de Branges spaces

The classical Kramer sampling theorem provides a method for obtaining orthogonal sampling formulas. In particular, when the involved kernel is analytic in the sampling parameter it can be stated in an abstract setting of reproducing kernel Hilbert spaces of entire functions which includes as a particular case the classical Shannon sampling theory. This abstract setting allows us to obtain a sort of converse result and to characterize when the sampling formula associated with an analytic Kramer kernel can be expressed as a Lagrange-type interpolation series. On the other hand, the de Branges spaces of entire functions satisfy orthogonal sampling formulas which can be written as Lagrange-type interpolation series. In this work some links between all these ideas are established.

Neuromorphic Detection of Vowel Representation Spaces

In this paper a layered architecture to spot and characterize vowel segments in running speech is presented. The detection process is based on neuromorphic principles, as is the use of Hebbian units in layers to implement lateral inhibition, band probability estimation and mutual exclusion. Results are presented showing how the association between the acoustic set of patterns and the phonologic set of symbols may be created. Possible applications of this methodology are to be found in speech event spotting, in the study of pathological voice and in speaker biometric characterization, among others.

How Blended Learning Reduce Underachievement in Higher Education: An Experience in Teaching Computer Sciences.

This paper presents a blended learning approach and a study evaluating instruction in a software engineering-related course unit as part of an undergraduate engineering degree program in computing. In the past, the course unit had a lecture-based format. In view of student underachievement and the high course unit dropout rate, a distance-learning system was deployed, where students were allowed to choose between a distance-learning approach driven by a moderate constructivist instructional model or a blended-learning approach. The results of this experience are presented, with the aim of showing the effectiveness of the teaching/learning system deployed compared to the lecture-based system previously in place. The grades earned by students under the new system, following the distance-learning and blended-learning courses, are compared statistically to the grades attained in earlier years in the traditional face-to-face classroom (lecture-based) learning.

Spaces of the Past, Histories of the Present: An Interview with Stuart Elden and Derek Gregory

The ontologies of space and territory, our experience of them and the techniques we use to govern them, the very conception of the socio-spatial formations that we inhabit, are all historically specific: they depend on a genealogy of practices, knowledges, discourses, regulations, performances and representations articulated in a way that is extremely complex yet nevertheless legible over time. In this interview we look at the logic and the patterns that intertwine space and time — both as objects and tools of inquiry — though a cross-disciplinary dialogue. The discussion with Stuart Elden and Derek Gregory covers the place of history in socio-spatial theory and in their own work, old and new ways of thinking about the intersection between history and territory, space and time, the implications of geography and history for thinking about contemporary politics, and the challenges now faced by critical thought and academic work in the current neo-liberal attack on public universities and the welfare state