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.

Computerized Interactive Orthodontic Treatment Planning

Submitted in partial fulfillment of the requirements for a Certificate in Orthodontics, Dept. of Orthodontics, University of Connecticut Health Center, 1975.

Evaluation of the association between cryptosporidiosis outbreaks and two interactive water fountain parks: Epidemiologic analysis and implications for public health

Background. A community-wide outbreak of cryptosporidiosis occurred in Dallas County during the summer of 2008. A subset of cases occurring with onset of illness within a 2 week interval was epidemiologically linked to 2 neighborhood interactive water fountain parks. ^ Methods. A case control study was conducted to evaluate risk factors associated with developing illness with cryptosporidiosis from the fountain parks. Cases were selected from a line list from the epidemiological study. The selection for the controls was either healthy family members or a daycare center nearby. Cases and controls were not matched. ^ Results. Interviews were completed for 44 fountain park attendees who met case definition and 54 community controls. Twenty-seven percent (27.3%) of the cases and 13.0% of the controls were between the ages of 0–4 years. Thirty-nine percent (38.6%) of the cases and 24.1% of the controls were between the ages of 5–13 years. Fourteen percent (13.6%) of the cases and 33.3% of the controls were between the ages of 14–31 years. Twenty percent (20.5%) of the cases and 29.6% of the controls were between the ages of 32–63 years. 47.7% of the cases and 42.6% of the controls were males. Fountain park attendees who reported having been splashed in the face with water were 10 times more likely to become ill than controls (OR = 10.0, 95% CI = 2.8–35.1). Persons who reported having swallowed water from the interactive fountains were 34 times more likely to become ill than controls (OR = 34.3, 95%CI = 9.3–125.7). ^ Conclusion. Prompt reporting of cases, identification of outbreak sources, and immediate implementation of remediation measures were critical in curtailing further transmission from these particular sites through the remainder of the season. This investigation underscores the potential for cryptosporidiosis outbreaks to occur in interactive fountain parks, and the need for enhanced preventive measures in these settings. Education of the public regarding avoidance of behaviors such as drinking water from interactive fountains is also an important component of public health prevention efforts. ^

An interactive intervention to impact adherence to antiretroviral treatment among treatment-naive HIV-infected adults in Thailand: A pilot randomized controlled study

Background. Consistent adherence to antiretroviral treatment is necessary for a treatment success. Improving and maintaining adherence rate >95% are challenging for health care professionals. This pilot randomized controlled study aimed to evaluate the impact of the interactive intervention on adherence to GPO-VIR, to describe the feasibility of the interactive intervention in Thailand, and to illustrate the adherence self-efficacy concept among HIV treatment-naïve patients in Thailand who were starting antiretroviral treatment. ^ Methods. The study took place at three HIV clinics located in Phayao, Thailand. Twenty-three patients were randomly assigned into the experimental (n=11) and the control groups (n=12). Each participant in the experimental group and a significant person to the patient received 5 educational sessions with a nurse at the clinics and at their homes. They also received 3 follow-up evaluations during the 6-month period of the study. The participants in the control group received the standard of care provided by HIV clinical personnel plus three follow-up evaluations at the clinic. ^ Results. Seventeen patients (7 in the experimental and 10 in the control group) completed the study. The 4-day recall on the Thai ACTG Adherence Scale demonstrated adherence rate >95% for most participants from both groups. After the first measurement, no experimental group patients reporting missing ART, while one control group participant continuously skipped ART. Participants from both groups had significantly increased CD4 cell counts after the study (F(1, 15) = 29.30, p = .000), but no differences were found between two groups (F(1, 15) = .001, p = .98). Examination of the intervention showed limitations and possibilities to implement it in Thailand. Qualitative data demonstrated self-efficacy expectations, resignation and acceptance as related concepts to improve adherence outcomes. ^ Conclusions. This interactive intervention, after appropriate modifications, is feasible to apply for Thai HIV-treatment naïve patients. Because of limitations the study could not demonstrate whether the interactive intervention improved adherence to ART among HIV-treatment naïve in Thailand. A longitudinal study in a larger sample would be required to test the impact of the intervention. ^ Keyword: antiretroviral treatment, adherence, treatment-naïve, Thailand, randomized controlled study ^

Model of interactive visualization of diffusion processes from different strains, and source routes and spatial diffusion of capuchin monkeys over the past 6 million years

Source routes and Spatial Diffusion of capuchin monkeys over the past 6 million years, rebuilt in the SPREAD 1.0.6 from the MCC tree. The map shows the 10 different regions to which distinctive samples were associated. The different transmission routes have been calculated from the average rate over time. Only rates with Bayes factor> 3 were considered as significantly different from zero. Significant diffusion pathways are highlighted with color varying from dark brown to red, being the dark brown less significant rates and deep red the most significant rates.

Interactive effects of salinity and elevated CO2 levels on juvenile eastern oysters, Crassostrea virginica

Rising levels of atmospheric CO2 lead to acidification of the ocean and alter seawater carbonate chemistry, which can negatively impact calcifying organisms, including mollusks. In estuaries, exposure to elevated CO2 levels often co-occurs with other stressors, such as reduced salinity, which enhances the acidification trend, affects ion and acid-base regulation of estuarine calcifiers and modifies their response to ocean acidification. We studied the interactive effects of salinity and partial pressure of CO2 (PCO2) on biomineralization and energy homeostasis in juveniles of the eastern oyster, Crassostrea virginica, a common estuarine bivalve. Juveniles were exposed for 11 weeks to one of two environmentally relevant salinities (30 or 15 PSU) either at current atmospheric PCO2 (400 µatm, normocapnia) or PCO2 projected by moderate IPCC scenarios for the year 2100 (700-800 µatm, hypercapnia). Exposure of the juvenile oysters to elevated PCO2 and/or low salinity led to a significant increase in mortality, reduction of tissue energy stores (glycogen and lipid) and negative soft tissue growth, indicating energy deficiency. Interestingly, tissue ATP levels were not affected by exposure to changing salinity and PCO2, suggesting that juvenile oysters maintain their cellular energy status at the expense of lipid and glycogen stores. At the same time, no compensatory upregulation of carbonic anhydrase activity was found under the conditions of low salinity and high PCO2. Metabolic profiling using magnetic resonance spectroscopy revealed altered metabolite status following low salinity exposure; specifically, acetate levels were lower in hypercapnic than in normocapnic individuals at low salinity. Combined exposure to hypercapnia and low salinity negatively affected mechanical properties of shells of the juveniles, resulting in reduced hardness and fracture resistance. Thus, our data suggest that the combined effects of elevated PCO2 and fluctuating salinity may jeopardize the survival of eastern oysters because of weakening of their shells and increased energy consumption.

Interactive effects of light, nitrogen source, and carbon dioxide on energy metabolism in the diatom Thalassiosira pseudonana

Due to the ongoing effects of climate change, phytoplankton are likely to experience enhanced irradiance, more reduced nitrogen, and increased water acidity in the future ocean. Here, we used Thalassiosira pseudonana as a model organism to examine how phytoplankton adjust energy production and expenditure to cope with these multiple, interrelated environmental factors. Following acclimation to a matrix of irradiance, nitrogen source, and CO2 levels, the diatom's energy production and expenditures were quantified and incorporated into an energetic budget to predict how photosynthesis was affected by growth conditions. Increased light intensity and a shift from inline image to inline image led to increased energy generation, through higher rates of light capture at high light and greater investment in photosynthetic proteins when grown on inline image. Secondary energetic expenditures were adjusted modestly at different culture conditions, except that inline image utilization was systematically reduced by increasing pCO2. The subsequent changes in element stoichiometry, biochemical composition, and release of dissolved organic compounds may have important implications for marine biogeochemical cycles. The predicted effects of changing environmental conditions on photosynthesis, made using an energetic budget, were in good agreement with observations at low light, when energy is clearly limiting, but the energetic budget over-predicts the response to inline image at high light, which might be due to relief of energetic limitations and/or increased percentage of inactive photosystem II at high light. Taken together, our study demonstrates that energetic budgets offered significant insight into the response of phytoplankton energy metabolism to the changing environment and did a reasonable job predicting them.