The Design of XML-Based Model and Experiment Description Languages for Network Simulation

The Simulation Automation Framework for Experiments (SAFE) is a project created to raise the level of abstraction in network simulation tools and thereby address issues that undermine credibility. SAFE incorporates best practices in network simulationto automate the experimental process and to guide users in the development of sound scientific studies using the popular ns-3 network simulator. My contributions to the SAFE project: the design of two XML-based languages called NEDL (ns-3 Experiment Description Language) and NSTL (ns-3 Script Templating Language), which facilitate the description of experiments and network simulationmodels, respectively. The languages provide a foundation for the construction of better interfaces between the user and the ns-3 simulator. They also provide input to a mechanism which automates the execution of network simulation experiments. Additionally,this thesis demonstrates that one can develop tools to generate ns-3 scripts in Python or C++ automatically from NSTL model descriptions.

Botanical drugs, synergy, and network pharmacology: forth and back to intelligent mixtures

For centuries the science of pharmacognosy has dominated rational drug development until it was gradually substituted by target-based drug discovery in the last fifty years. Pharmacognosy stems from the different systems of traditional herbal medicine and its "reverse pharmacology" approach has led to the discovery of numerous pharmacologically active molecules and drug leads for humankind. But do botanical drugs also provide effective mixtures? Nature has evolved distinct strategies to modulate biological processes, either by selectively targeting biological macromolecules or by creating molecular promiscuity or polypharmacology (one molecule binds to different targets). Widely claimed to be superior over monosubstances, mixtures of bioactive compounds in botanical drugs allegedly exert synergistic therapeutic effects. Despite evolutionary clues to molecular synergism in nature, sound experimental data are still widely lacking to support this assumption. In this short review, the emerging concept of network pharmacology is highlighted, and the importance of studying ligand-target networks for botanical drugs is emphasized. Furthermore, problems associated with studying mixtures of molecules with distinctly different pharmacodynamic properties are addressed. It is concluded that a better understanding of the polypharmacology and potential network pharmacology of botanical drugs is fundamental in the ongoing rationalization of phytotherapy.

Optimized quantitative magnetic resonance spectroscopy for clinical routine

Several practical obstacles in data handling and evaluation complicate the use of quantitative localized magnetic resonance spectroscopy (qMRS) in clinical routine MR examinations. To overcome these obstacles, a clinically feasible MR pulse sequence protocol based on standard available MR pulse sequences for qMRS has been implemented along with newly added functionalities to the free software package jMRUI-v5.0 to make qMRS attractive for clinical routine. This enables (a) easy and fast DICOM data transfer from the MR console and the qMRS-computer, (b) visualization of combined MR spectroscopy and imaging, (c) creation and network transfer of spectroscopy reports in DICOM format, (d) integration of advanced water reference models for absolute quantification, and (e) setup of databases containing normal metabolite concentrations of healthy subjects. To demonstrate the work-flow of qMRS using these implementations, databases for normal metabolite concentration in different regions of brain tissue were created using spectroscopic data acquired in 55 normal subjects (age range 6-61 years) using 1.5T and 3T MR systems, and illustrated in one clinical case of typical brain tumor (primitive neuroectodermal tumor). The MR pulse sequence protocol and newly implemented software functionalities facilitate the incorporation of qMRS and reference to normal value metabolite concentration data in daily clinical routine. Magn Reson Med, 2013. © 2012 Wiley Periodicals, Inc.

Quantification of network perfusion in ASL cerebral blood flow data with seed based and ICA approaches

Independent component analysis (ICA) or seed based approaches (SBA) in functional magnetic resonance imaging blood oxygenation level dependent (BOLD) data became widely applied tools to identify functionally connected, large scale brain networks. Differences between task conditions as well as specific alterations of the networks in patients as compared to healthy controls were reported. However, BOLD lacks the possibility of quantifying absolute network metabolic activity, which is of particular interest in the case of pathological alterations. In contrast, arterial spin labeling (ASL) techniques allow quantifying absolute cerebral blood flow (CBF) in rest and in task-related conditions. In this study, we explored the ability of identifying networks in ASL data using ICA and to quantify network activity in terms of absolute CBF values. Moreover, we compared the results to SBA and performed a test-retest analysis. Twelve healthy young subjects performed a fingertapping block-design experiment. During the task pseudo-continuous ASL was measured. After CBF quantification the individual datasets were concatenated and subjected to the ICA algorithm. ICA proved capable to identify the somato-motor and the default mode network. Moreover, absolute network CBF within the separate networks during either condition could be quantified. We could demonstrate that using ICA and SBA functional connectivity analysis is feasible and robust in ASL-CBF data. CBF functional connectivity is a novel approach that opens a new strategy to evaluate differences of network activity in terms of absolute network CBF and thus allows quantifying inter-individual differences in the resting state and task-related activations and deactivations.

Visualization Techniques For The Analysis Of Network Simulation Results

The Simulation Automation Framework for Experiments (SAFE) streamlines the de- sign and execution of experiments with the ns-3 network simulator. SAFE ensures that best practices are followed throughout the workflow a network simulation study, guaranteeing that results are both credible and reproducible by third parties. Data analysis is a crucial part of this workflow, where mistakes are often made. Even when appearing in highly regarded venues, scientific graphics in numerous network simulation publications fail to include graphic titles, units, legends, and confidence intervals. After studying the literature in network simulation methodology and in- formation graphics visualization, I developed a visualization component for SAFE to help users avoid these errors in their scientific workflow. The functionality of this new component includes support for interactive visualization through a web-based interface and for the generation of high-quality, static plots that can be included in publications. The overarching goal of my contribution is to help users create graphics that follow best practices in visualization and thereby succeed in conveying the right information about simulation results.

Clinical, polysomnographic and genome-wide association analyses of narcolepsy with cataplexy: a European Narcolepsy Network study

The aim of this study was to describe the clinical and PSG characteristics of narcolepsy with cataplexy and their genetic predisposition by using the retrospective patient database of the European Narcolepsy Network (EU-NN). We have analysed retrospective data of 1099 patients with narcolepsy diagnosed according to International Classification of Sleep Disorders-2. Demographic and clinical characteristics, polysomnography and multiple sleep latency test data, hypocretin-1 levels, and genome-wide genotypes were available. We found a significantly lower age at sleepiness onset (men versus women: 23.74 ± 12.43 versus 21.49 ± 11.83, P = 0.003) and longer diagnostic delay in women (men versus women: 13.82 ± 13.79 versus 15.62 ± 14.94, P = 0.044). The mean diagnostic delay was 14.63 ± 14.31 years, and longer delay was associated with higher body mass index. The best predictors of short diagnostic delay were young age at diagnosis, cataplexy as the first symptom and higher frequency of cataplexy attacks. The mean multiple sleep latency negatively correlated with Epworth Sleepiness Scale (ESS) and with the number of sleep-onset rapid eye movement periods (SOREMPs), but none of the polysomnographic variables was associated with subjective or objective measures of sleepiness. Variant rs2859998 in UBXN2B gene showed a strong association (P = 1.28E-07) with the age at onset of excessive daytime sleepiness, and rs12425451 near the transcription factor TEAD4 (P = 1.97E-07) with the age at onset of cataplexy. Altogether, our results indicate that the diagnostic delay remains extremely long, age and gender substantially affect symptoms, and that a genetic predisposition affects the age at onset of symptoms.

UAVNet: A Mobile Wireless Mesh Network Using Unmanned Aerial Vehicles

We developed UAVNet, a framework for the autonomous deployment of a flying Wireless Mesh Network using small quadrocopter-based Unmanned Aerial Vehicles (UAVs). The flying wireless mesh nodes are automatically interconnected to each other and building an IEEE 802.11s wireless mesh network. The implemented UAVNet prototype is able to autonomously interconnect two end systems by setting up an airborne relay, consisting of one or several flying wireless mesh nodes. The developed software includes basic functionality to control the UAVs and to setup, deploy, manage, and monitor a wireless mesh network. Our evaluations have shown that UAVNet can significantly improve network performance.

Complementary and conventional medicine in Switzerland: comparing characteristics of general practitioners

OBJECTIVES: Do structural characteristics of general practitioners (GPs) who practice complementary medicine (CAM) differ from those GPs who do not? Assessed characteristics included experience and professional integration of general practitioners (GPs), workload, medical activities, and personal and technical resources of practices. The investigated CAM disciplines were anthroposophic medicine, homoeopathy, traditional Chinese medicine, neural therapy and herbal medicine. MATERIAL AND METHODS: We designed a cross-sectional study with convenience and stratified samples of GPs providing conventional (COM) and/or complementary primary care in Switzerland. The samples were taken from the database of the Swiss medical association (FMH) and from CAM societies. Data were collected using a postal questionnaire. RESULTS: Of the 650 practitioners who were included in the study, 191 were COM, 167 noncertified CAM and 292 certified CAM physicians. The proportion of females was higher in the population of CAM physicians. Gender-adjusted age did not differ between CAM and COM physicians. Nearly twice as many CAM physicians work part-time. Differences were also seen for the majority of structural characteristics such as qualification of physicians, type of practice, type of staff, and presence of technical equipment. CONCLUSION: The study results show that structural characteristics of primary health care do differ between CAM and COM practitioners. We assumed that the activities of GPs are defined essentially by analyzed structures. The results are to be considered for evaluations in primary health care, particularly when quality of health care is assessed.

Testing strategies and follow-up for coeliac disease in a general internal medicine outpatient department from 2000 to 2005

PRINCIPLES: Coeliac disease (gluten sensitive enteropathy) is a genetically determined disorder with an incidence in the general population that is comparable to type 2 diabetes mellitus. Awareness of this fact and of the often atypical and oligosymptomatic manifestations is only now gaining ground in the medical profession. A high index of suspicion is important in order to minimise diagnostic and therapeutic delay. METHODS: Testing patterns and follow-up for coeliac disease in our institution have been analysed retrospectively for the past five years. The current literature was reviewed with respect to recommendations for clinical practice. RESULTS: A total of 271 patients were tested for coeliac disease over a period of five years. Only in 24 patients were positive results found; after further work-up, the final number of cases with certain or presumed coeliac disease was four. Followup was often difficult, many patients being lost after a single visit. CONCLUSIONS: This study showed that the number of tests ordered in our institution, more often for abdominal than atypical symptoms, has started to increase in the past two years. It also showed that screening tests have found their place in general clinical practice, while the final choice of tests needs to be determined in accordance with available guidelines and local resources. Upper endoscopy with small bowel biopsy remains the gold standard for diagnosis, but its place in follow-up is less certain. Coeliac disease is a disorder for which there is a definite treatment (gluten free diet); if it is left untreated diminished quality of life and potentially serious complications may ensue. Further education of the medical profession regarding coeliac disease, its incidence, presentation and treatment, is clearly indicated..

The supply of complementary and alternative medicine in Swiss hospitals

OBJECTIVES: Over the past few years, a considerable increase in complementary and alternative medicine (CAM) has been observed, particularly in primary care. In contrast little is known about the supply of CAM in Swiss hospitals. This study aims at the investigation of amount and structure of CAM activities of Swiss hospitals. MATERIALS AND METHODS: We designed a cross-sectional survey using a 2-step, questionnaire- based approach acquiring overview information form hospital managers in a first questionnaire leading to detailed information on CAM usage at medical department level (head of department). This second questionnaire provides data of physician-based and non-physician-based CAM supply. RESULTS: The size of hospitals was significantly associated with the provision of CAM. 33% of the hospital managers indicated 1 or more medical doctor (MD) using CAM in their hospital compared to 37% of confirmation on department level (Kappa value 0.5). Mostly different CAM methods were applied. Acupuncture was used most frequently. However only 13 hospitals (11%) occupied more than 3 CAM MDs and only 5 hospitals had more than 2 full-time equivalents for MDs. Furthermore, 74.7% of these personnel resources were dedicated for outpatient care. In terms of CAM methods anthroposophic medicine accounted for more than half of the total personnel costs. On the other hand usage of non-physician based CAM accounted for 41% according to hospital managers compared to 64% of CAM usage according to medical departments (Kappa values 0.31). Reflexology of the foot was used most frequently. CONCLUSION: Total supply of CAM in Swiss hospitals is low and concentrates on few hospitals. Acupuncture is the widest spread discipline but anthroposophic medicine spends the most resources. The study shows that a high patient demand for CAM faces low supply in hospitals.