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Every year, hundreds of thousands of patients are affected by treatment failure or adverse drug reactions, many of which could be revented by pharmacogenomic testing. To address these deficiencies in care, clinics require
automated clinical decision support through computer based systems, which provide clinicians with patient-specific ecommendations. The primary knowledge needed for clinical pharmacogneomics is currently being
developed through textual and unstructured guidelines.
In this thesis, it is evaluated whether a web service can annotate clinically relevant genetic variants with guideline information using web services and identify areas of challenge. The proposed tool displays a formal representation of pharmacogenomic guideline information through a web service and existing resources. It enables the annotation of variant call format (VCF) files with clinical guideline information from the Pharmacogenomic Knowledge Base (PharmGKB) and Clinical Pharmacogenetics Implementation Consortium (CPIC).
The applicability of the web service to nnotate clinically relevant variants with pharmacogenomics guideline information is evaluated by translating five guidelines to a web service workflow and executing the process to annotate publically available genomes. The workflow finds genetic variants covered in CPIC guidelines and influenced drugs.
The results show that the web service could be used to annotate in real time clinically relevant variants with up-to-date pharmacogenomics guideline information, although several challenges such as translating variants into star allele nomenclature and the absence of a unique haplotype nomenclature
remain before the clinical implementation of this approach and the use on other drugs.
There are many drug interactions and to know every single interaction is impossible. In Uganda, a country located in East Africa, patients often do not get a patient information leflaet when a physician prescribes drugs because they only get the drugs without packaging and information inside. Even in developed countries many poeple die because of drug interactions.
This work aims at developing a clinical decision support system for different kinds of drug interactions: 1) drug-drug interaction,
2) drug-food interactions,
3) drug-condition
interactions and
4) drug-disease interactions.
This system must be integrated into an
existing hospital information system called electronic Health Management Information System (eHMIS).
In the first part of this thesis different kinds of clinical decision support systems are described to find out which one is the best for eHMIS. The two different types are knowledge-based and non knowledge-based systems. The second part of this thesis, the data base of eHMIS is extended to have a full
knowledge base for the new module which contains drug-drug interactions, drug-food interactions, drug-disease interactions as well as drug-condition interactions. Therefore new tables were created and filled with data of several data bases with drug interactions. The last part is about designing the clinical decision support system for drug interactions
with the knowledge base of eHMIS, including the implementation considering the integration into the existing system. To know how health professionals in Uganda work
with an electronical health system as well as their other work ows was important. The system now runs in a hospital in Kampala, the capital of Uganda and in a health center level three in Mifumi, a village located in the east of the country.
Background: Stroke rehabilitation is a complex process that requires collaboration between stroke patients
and various health professionals. One important component of the rehabilitation is to set goals collaboratively with health professionals. The goal setting process can be time-consuming. In many cases, it is complicated for the patient and difficult to track for the health professionals. A simple user interface that supports patients, their family members and health professionals can help both sides to make the goal setting and attainment process easier.
Objectives: The aim is to design and develop a software for the goal attainment process of stroke patients with milder disabilities that facilitates goal setting process and the traceability of the goal progress for patients and health professionals.
Methods: Based on previous evaluated results, the web interface was developed and improved. Using this knowledge, a goal setting interface was added. To analyze the the goal setting process, goal attainment scaling (GAS) was included as well as parts of the International Classification of Functioning, Disability and Health (ICF) core set for stroke. The results were discussed afterwards in focus groups and evaluated based on two stroke patients, one family member and health professionals.
Results: We developed an interactive prototype, that can aid the rehabilitation at home by inserting
problems with ICF codes and different kinds of goals, creating new activities and tracing goal progress by reviewing the different goals. With the help of the GAS the outcome of the patient’s goals are visualized by a line chart presenting the positive or negative outcomes of the stroke rehabilitation.
Conclusion: The interactive prototype showed that it can support stroke patients during their rehabilitation
at home. A usability test indicated that the goal setting and attainment process was perceived as useful for patients and their family members. Small improvements have to be made to simplify use and error handling. For health professionals, the prototype could also simplify the documentation process by using ICF in the prototype, and also improving collaboration when using the tool for coordination.
An architectural concept for implementing the socio-technical workflow of Digital Pathology in Chile
(2014)
Virtual Microscopy opens up the possibility to remotely access high quality images at large scales for scientific research, education, and clinical application. For clinical diagnostics, Digital Pathology (DP) presents a novel opportunity to reduce variability [Bauer et al., 2013] due to the reproducible access to Whole Slide Imaging, quantitative parameters (e.g. HER2 stained membrane) [Al-Janabi et al., 2012], second opinion and Quality Assurance [Ho et al., 2013]. Despite of the mentioned advantages, the challenge remains to incorporate DP into the pathologists workflow within a heterogeneous environment of systems and infrastructures [Stathonikos
et al., 2013]. Different issues must be solved in order to optimize the impact of DP in the daily clinical practice [Daniel et al., 2012] [Ho et al., 2006]. The integration needs precise planning and comprehensive evaluation for adopting this technology
[Stathonikos et al., 2013]. This thesis will focus on an organizational development approach based on a Socio-Technical System (STS). The socio-technical approach covers: (i) the technical issue: tissue-scanner, NDP.view, NDP.serve, analysis software, and (ii) the social issue: pathologists, technicians. In order to improve the integration, a joint optimization (of i and ii) is necessary. The developed STS approach will optimize the integration of DP towards improved workflows in clinical environments. The improved workflows will reduce the pathologists turnaround time, improve the certainty of the diagnostics, and provide a more effective patient care within the covered institutions. An overt multi-site Participatory Observation, Questionnaires, and Business Process Modelling Notation will be used to analyse the existing pathological workflows. Based on this, the system will be modelled with the 3lgm2 Toolkit [Winter et al., 2007] under consideration of various technical subsystems that are present in the clinical environment. Afterwards, the interfaces between subsystems and its possible interoperabilities will be evaluated, taking into account the different existing standards and guidelines for image processing and management, as well as business processes in DP. In order to analyse the existing preconditions a questionnaire will be evaluated to establish a robust and valid view. In addition, the overt participatory observation will support this elevation, giving a deeper insight on the social part. This observation also covers the technical side including the whole pathological process. The socio technical model will then reveal measurable potential for optimization with incorporated DP (e.g. higher throughput for slides). The organizational development approach consists of a Socio-Technical System based on overt multi-site participatory observations, questionnaires, business process modelling and 3LGM2, will optimize the use of Digital Pathology in the daily clinical practice and raise the acceptance to incorporate integrate the new technology within the dayly workflow through the user centred process of incorporation.
• Perform and evaluate a questionnaire and a participant observation of pathologists work days in private & public institutions
• Create and evaluate a 3lgm2 model
• Model the current pathological process (viewpoint of pathologist & technical assistant) & perform and evaluate a contextual inquiry to elevate the pathologists requirements & expectations towards the system
• Test the future WF according the model parameters.
This project will detect unsuspected interrelations and interdependencies within the socio- technical workflow with a pathology laboratory. The observation will reveal the action conformity as well as the environment in which the process has to be embedded. Furthermore it will establish an optimized workflow for a specific clinical environment to prepare the implementation of DP. Additionally it will be possible to
quantify digitized images in order to improve decision making and lastly to improve patient care. In the future it will be possible to extend automated image analysis in order to support clinical decision support. Depending on acceptance, this can lead towards an automated clinical decision support for cases with low complexity.
The aim of this master’s thesis is the design and implementation of a dedicated software system, for planning and implementation of occupational therapy intervention and research studies, in a driving simulator environment. In the first part, the concept based on user requirements is presented. It consists of architectural patterns and guidelines with the main focus on utility and application security. The result of this part is the design of a web application which supports integration in a clinical as well as a research environment. The second part presents the reference implementation of the previously introduced concept. It was developed under a case study in a research facility which hosts a driving simulator. A close cooperation and the influence the researcher’s experience led into a product which provides advanced usability for the target users. In conclusion, the thesis validated the concept indirectly under a testing phase of the reference implementation. It provides the base for a follow-up project to refine the software product and extend the concept to different fields of application.
The Greifswald University Hospital in Germany conducts a research project called "Greifswald Approach to Individualized Medicine (GANI_MED)", which aims at improving patient care through personalized medicine. As a result of this project, there are multiple regional patient cohorts set up for different common diseases. The collected data of these cohorts will act as a resource for epidemiological research. Researchers are going to get the possibility to use this data for their study, by utilizing a variety of different descriptive metadata attributes. The actual medical datasets of the patients are integrated from multiple clinical information systems and medical devices. Yet, at this point in the process of defining a research query, researchers do not have proper tools to query for existing patient data. There are no tools available which offer a metadata catalogue that is linked to observational data, which would allow convenient research. Instead, researchers have to issue an application for selected variables that fit the conditions of their study, and wait for the results. That leaves the researchers not knowing in advance, whether there are enough (or any) patients fitting the specified inclusion and exclusion criteria. The "Informatics for Integrating Biology and the Bedside (i2b2)" framework has been assessed and implemented as a prototypical evaluation instance for solving this issue. i2b2 will be set up at the Institute for Community Medicine (ICM) at Greifswald, in order to act as a preliminary query tool for researchers. As a result, the development of a research data import routine and customizations of the i2b2 webclient were successfully performed. An important part of the solution is, that the metadata import can adapt to changes in the metadata. New metadata items can be added without changing the import program. The results of this work are discussed and a further outlook is described in this thesis.
Ambulant studies are dependent on the behavior and compliance of subjects in their home environment. Especially during interventions on the musculoskeletal system, monitoring physical activity is essential, even for research on nutritional, metabolic, or neuromuscular issues. To support an ambulant study at the German Aerospace Center (DLR), a pattern recognition system for human activity was developed. Everyday activi-ties of static (standing, sitting, lying) and dynamic nature (walking, ascending stairs, descending stairs, jogging) were under consideration. Two tri-axial accelerometers were attached to the hip and parallel to the tibia. Pattern characterizing features from the time domain (mean, standard deviation, absolute maximum) and the frequency domain (main frequencies, spectral entropy, autoregressive coefficients, signal magni-tude area) were extracted. Artificial neural networks (ANN) with a feedforward topology were trained with backpropagation as supervised learning algorithm. An evaluation of the resulting classifier was conducted with 14 subjects completing an activity protocol and a free chosen course of activities. An individual ANN was trained for each subject. Accuracies of 87,99 % and 71,23 % were approached in classifying the activity protocol and the free run, respectively. Reliabilities of 96,49 % and 76,77 % were measured. These performance parameters represent a working ambulant physical activity monitor-ing system.
Aside from hardware, a major component of a Brain Computer Interface is the software that provides the tools for translating raw acquired brain signals into commands to control an application or a device. There’s a range of software, some proprietary, like MATLAB and some free and open source (FOSS), accessible under the GNU General Public License (GNU GPL). OpenViBE is one such freely accessible software. This thesis carries out a functionality and usability test of the platform, looking at its portability, architecture and communication protocols. To investigate the feasibility of reproducing the P300 xDAWN speller BCI presented by OpenViBE, users focused on a character on a 6x6 alphanumeric grid which contained a sequence of random flashes of the rows and columns. Visual stimulus is presented to a user every time the character they are focusing on is highlighted in a row or column. A TMSi analog-to-digital converter was used together with a 32-channel active electrode cap (actiCAP) to record user’s Electroencephalogram (EEG) which was then used in an offline session to train the spatial filter algorithm, and the classifier to identify the P300 evoked potentials, elicited as a user’s reaction to an external stimulus. In an online session, the users tried to spell with the application using the power of their brain signal. Aspects of evoked potentials (EP), both auditory (AEP) and visual (VEP) are further investigated as a validation of results of the P300 speller.
Clinical diagnosis ideally relies on quantitative measures of disease. For a number of diseases, diagnostic guidelines require or at least recommend neuroimaging exams to support the clinical findings. As such, there is also an increasing interest to derive quantitative results from magnetic resonance imaging (MRI) examinations, i.e. images providing quantitative T1, T2, T2* tissue parameters. Quantitative MRI protocols, however, often require prohibitive long acquisition times (> 10 minutes), nor standards have been established to regulate and control MRI-based quantification. This work aims at exploring the technical feasibility to accelerate existing MRI acquisition schemes to enable a -3 minutes clinical imaging protocol of quantitative tissue parameters such as T2 and T2* and at identifying technical factors that are key elements to obtain accurate results. In the first part of this thesis, the signal model of an existing quantitative T2-mapping algorithm is expanded to explore the methodology for a broader use including the application to T2* and its use in the presence of imperfect imaging conditions and system related limitations of the acquisition process. The second part of this thesis is dedicated to optimize the iterative mapping algorithm for a robust clinical application including the integration on a clinical MR platform. This translation of technology is a major step to enable and validate such new methodology in a realistic clinical environment. The robustness and accuracy of the developed and implemented model is investigated by comparing with the "gold standard" information from fully sampled phantom and in-vivo MRI data.
Quantitative assessment of Positron Emission Tomography (PET) imaging can be used for diagnosis and staging of tumors and monitoring of response in cancer treatment. In clinical practice, PET analysis is based on normalized indices such as those based on the Standardized Uptake Value (SUV). Although largely evaluated, these indices are considered quite unstable mainly because of the simplicity of their experimental protocol. Development and validation of more sophisticated methods for the purposes of clinical research require a common open platform that can be used both for prototyping and sharing of the analysis methods, and for their evaluation by clinical users. This work was motivated by the lack of such platform for longitudinal quantitative PET analysis. By following a prototype driven software development approach, an open source tool for quantitative analysis of tumor changes based on multi-study PET image data has been implemented. As a platform for this work, 3D Slicer 4, a free open source software application for medical image computing has been chosen. For the analysis and quantification of PET data, the implemented software tool guides the user through a series of workflow steps. In addition to the implementation of a guided workflow, the software was made extensible by integration of interfaces for the enhancement of segmentation and PET quantification algorithms. By offering extensibility, the PET analysis software tool was transformed into a platform suitable for prototyping and development of PET-specific segmentation and quantification methods. The accuracy, efficiency and usability of the platform were evaluated in reproducibility and usability studies. The results achieved in these studies demonstrate that the implemented longitudinal PET analysis software tool fulfills all requirements for the basic quantification of tumors in PET imaging and at the same time provides an efficient and easy to use workflow. Furthermore, it can function as a platform for prototyping of PET-specific segmentation and quantification methods, which in the future can be incorporated in the workflow.
Background: An important factor in approaching the challenges of chronic diseases, requiring long-term management and high costs, is the active participation of the patient in the care process. Objectives: Facing the problem of lacking patient-tailored, comprehensive health management software, the aim of this thesis is to generate ideas for a graphical user interface (GUI) to support stroke patients in the management of their individual care process. The objectives are to prototype a GUI for a patient e-service and to evaluate its usefulness and usability with stroke patients. Methods: A scenario-based, user-centered design method was used to envision ideas for the user interface. Static prototypes were realized with the tool Pencil and for the implementation of a dynamic prototype web programming techniques were used. For the evaluation of the prototypes the methods of focus group discussion and cooperative evaluation were applied. Results: The situation of a representative stroke patient and his interaction with the e-service were described in scenarios. Graphical user interfaces of the involved system views were derived from the scenarios and illustrated with static wireframe prototypes. A welcome screen, a care process timeline overview, and a diary with data sharing functionality were designed. The diary functionality was further examined by implementing a prototypical web application. During the evaluation, feedback for further improvements was gathered, and assumptions about the user information and functionality needs could be verified. Conclusion: The developed prototypes represent a suitable graphical user interface and visualizations to support stroke patients in the management of their care process. An overview of appointments on the welcome screen, a diary to document and monitor health, a timeline overview of all time-related health information and a selected sharing functionality were found to be important features of a personal health system for stroke patients.
In this thesis a software system is proposed that provides transparent access to dynamically processed data using a synthetic filesystem for the data transfer as well as interaction with the processing pipeline. Within this context the architecture for such a software solution has been designed and implemented. Using this implementation various profiling measurements have been acquired in order to evaluate the applicability in different data processing scenarios. Usability aspects, considering the interaction with the processing pipeline, have been examined as well. The implemented software is able to generate the processing result on-the-fly without modification of the original input data. Access to the output data is provided by means of a common filesystem interface without the need of implementing yet another communication protocol. Within the processing pipeline the data can be accessed and modified independently from the actual input and output encoding. Currently the data can be modified using a C/C++, GLSL or Java front end. Profiling data has shown that the overhead induced by the filesystem is negligible for most usage patterns and is only critical for realtime processing with a high data throughput e. g. video processing at or above 30 frames per second where typically no file operations are involved.
Segmentation of the Cerebrospinal Fluid from MRI Images for the Treatment of Disc Herniations
(2010)
About 80 percent of people are affected at some point in their lives by lower back pain, which is one of the most common neurological diseases and reasons for long-term disability in the United States. The symptoms are primarily caused by overly heavy lifting and/or overstretching of the back, leading to a rupture and an outward bulge of an intervertebral disc, which puts pressure on and pinches the nerve fibers of the spine. The most common form is a lumbar disc herniation between the fourth and fifth lumbar vertebra and between the fifth lumbar vertebra and the sacrum. In recent years the diagnosis of lower back pain has improved, mainly due to enhanced imaging techniques and imaging quality, but the surgical therapy remains hazardous. Reasons for this include low visibility when accessing the lumbar area and the high risk of causing permanent damage when touching the nerve fibers. A new approach for increasing patient safety is the segmentation and visualization of the cerebrospinal fluid in the lower lumbar region of the vertebral column. For this purpose a new fully-automatic and a semi-automatic approach were developed for separating the cerebrospinal fluid from its surroundings on T2-weighted MRI scans of the lumbar vertebra. While the fully-automatic algorithm is realized by a model-based searching method and a volume-based segmentation, the semi-automatic algorithm requires a seed point and performs the segmentation on individual axial planes through a combination of a region-based segmentation algorithm and a thresholding filter. Both algorithms have been applied to four T2-weighted MRI datasets and are compared with a gold-standard segmentation. The segmentation overlap with the gold-standard was 78.7 percent for the fully-automatic algorithm and 93.1 percent for the semi-automatic algorithm. In the pathological region the fully-automatic algorithm obtained a similarity of 56.6 percent, compared to 87.8 percent for the semi-automatic algorithm.
This thesis presents a photmetric stereo method based on the work of Schulze [35], who in turn extended the research of Schroeder et al. [33,34] In this approach, three different lightings are obtained by illuminating the object by three colored light sources (red, green and blue). A video of the subject is captured from the front, the back and the side. The single frames are then extracted from the viedo, which are used for the 3D reconstruction of the subject. The aim of this work was to improve the presented method of Schulze with real patient subjects by getting a better sphere calibration and changing some parameters in the patient processing. As the graphical interface was implemented for persons with a technical background, it has been changed to become also more convenient to use for non-technically oriented staff
Access, Handling and Visualization Tools for Multiple Data Types for Breast Cancer Decision Support
(2011)
Breast cancer is the most commonly diagnosed cancer among U.S women, besides skin cancer. More than 1 in 4 cancers among women are breast cancer. And though death rates have been decreasing since 1990, about 40,170 women in the U.S. were expected to die in 2009 from breast cancer. The progress of molecular profiling, in the last decade has revolutionized the understanding of cancer, but also introduced more complexity with new data such as gene expression, copy number variation, mutations and DNA methylation. These new data open up the possibility of differential diagnosis, much more precise prognosis as well as prediction of therapy response than any of the diagnostic tools that are available in the current practice. Additionally, epidemiological databases store clinically relevant information on hundreds of thousands of patients. However, with the abundance of all this information, clinicians will need new tools to access and visualize such data and use the information gained to treat new patients. The general problem will be to access, filter and analyze the data and then visualize them in a clinical context. This data ranges from clinico-pathological information, to molecular profiles from highthroughput genomic measurements and imaging data. Furthermore, data from patient populations is aggregated on epidemiological level and can be found under numerous clinical studies.
Medication reconciliation is defined by the American Society of Health- System Pharmacists (ASHP) and the American Pharmacists Association (AphA) as “the comprehensive evaluation of a patient’s medication regimen any time there is a change in therapy in an effort to avoid medication errors such as omissions, duplications, dosing errors or drug interactions, as well as to observe compliance and adherence patterns “. Medication reconciliation is very important to avoid medication errors but it is also a complex and time-consuming process. Medication histories, i.e. records of prescription, purchase, and refill sequences are considered to be a resource from which conclusions about medication reconciliation can be drawn. However, medication histories spread across diverse paper and electronic media may lack the required accuracy. By employing multiple electronic sources this thesis will evaluate if more accurate medication histories can be collected.