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The IronChip evaluation package: a package of perl modules for robust analysis of custom microarrays
(2010)
Background: Gene expression studies greatly contribute to our understanding of complex relationships in gene regulatory networks. However, the complexity of array design, production and manipulations are limiting factors, affecting data quality. The use of customized DNA microarrays improves overall data quality in many situations, however, only if for these specifically designed microarrays analysis tools are available. Results: The IronChip Evaluation Package (ICEP) is a collection of Perl utilities and an easy to use data evaluation pipeline for the analysis of microarray data with a focus on data quality of custom-designed microarrays. The package has been developed for the statistical and bioinformatical analysis of the custom cDNA microarray IronChip but can be easily adapted for other cDNA or oligonucleotide-based designed microarray platforms. ICEP uses decision tree-based algorithms to assign quality flags and performs robust analysis based on chip design properties regarding multiple repetitions, ratio cut-off, background and negative controls. Conclusions: ICEP is a stand-alone Windows application to obtain optimal data quality from custom-designed microarrays and is freely available here (see “Additional Files” section) and at: http://www.alice-dsl.net/evgeniy. vainshtein/ICEP/
Psycho-pathological conditions, such as depression or schizophrenia, are often accompanied by a distorted perception of time. People suffering from this conditions often report that the passage of time slows down considerably and that they are “stuck in time.” Virtual Reality (VR) could potentially help to diagnose and maybe treat such mental conditions. However, the conditions in which a VR simulation could correctly diagnose a time perception deviation are still unknown. In this paper, we present an experiment investigating the difference in time experience with and without a virtual body in VR, also known as avatar. The process of substituting a person’s body with a virtual body is called avatar embodiment. Numerous studies demonstrated interesting perceptual, emotional, behavioral, and psychological effects caused by avatar embodiment. However, the relations between time perception and avatar embodiment are still unclear. Whether or not the presence or absence of an avatar is already influencing time perception is still open to question. Therefore, we conducted a between-subjects design with and without avatar embodiment as well as a real condition (avatar vs. no-avatar vs. real). A group of 105 healthy subjects had to wait for seven and a half minutes in a room without any distractors (e.g., no window, magazine, people, decoration) or time indicators (e.g., clocks, sunlight). The virtual environment replicates the real physical environment. Participants were unaware that they will be asked to estimate their waiting time duration as well as describing their experience of the passage of time at a later stage. Our main finding shows that the presence of an avatar is leading to a significantly faster perceived passage of time. It seems to be promising to integrate avatar embodiment in future VR time-based therapy applications as they potentially could modulate a user’s perception of the passage of time. We also found no significant difference in time perception between the real and the VR conditions (avatar, no-avatar), but further research is needed to better understand this outcome.
The ecosystem of the high northern latitudes is affected by the recently changing environmental conditions. The Arctic has undergone a significant climatic change over the last decades. The land coverage is changing and a phenological response to the warming is apparent. Remotely sensed data can assist the monitoring and quantification of these changes. The remote sensing of the Arctic was predominantly carried out by the usage of optical sensors but these encounter problems in the Arctic environment, e.g. the frequent cloud cover or the solar geometry. In contrast, the imaging of Synthetic Aperture Radar is not affected by the cloud cover and the acquisition of radar imagery is independent of the solar illumination. The objective of this work was to explore how polarimetric Synthetic Aperture Radar (PolSAR) data of TerraSAR-X, TanDEM-X, Radarsat-2 and ALOS PALSAR and interferometric-derived digital elevation model data of the TanDEM-X Mission can contribute to collect meaningful information on the actual state of the Arctic Environment. The study was conducted for Canadian sites of the Mackenzie Delta Region and Banks Island and in situ reference data were available for the assessment. The up-to-date analysis of the PolSAR data made the application of the Non-Local Means filtering and of the decomposition of co-polarized data necessary.
The Non-Local Means filter showed a high capability to preserve the image values, to keep the edges and to reduce the speckle. This supported not only the suitability for the interpretation but also for the classification. The classification accuracies of Non-Local Means filtered data were in average +10% higher compared to unfiltered images. The correlation of the co- and quad-polarized decomposition features was high for classes with distinct surface or double bounce scattering and a usage of the co-polarized data is beneficial for regions of natural land coverage and for low vegetation formations with little volume scattering. The evaluation further revealed that the X- and C-Band were most sensitive to the generalized land cover classes. It was found that the X-Band data were sensitive to low vegetation formations with low shrub density, the C-Band data were sensitive to the shrub density and the shrub dominated tundra. In contrast, the L-Band data were less sensitive to the land cover. Among the different dual-polarized data the HH/VV-polarized data were identified to be most meaningful for the characterization and classification, followed by the HH/HV-polarized and the VV/VH-polarized data. The quad-polarized data showed highest sensitivity to the land cover but differences to the co-polarized data were small. The accuracy assessment showed that spectral information was required for accurate land cover classification. The best results were obtained when spectral and radar information was combined. The benefit of including radar data in the classification was up to +15% accuracy and most significant for the classes wetland and sparse vegetated tundra. The best classifications were realized with quad-polarized C-Band and multispectral data and with co-polarized X-Band and multispectral data. The overall accuracy was up to 80% for unsupervised and up to 90% for supervised classifications. The results indicated that the shortwave co-polarized data show promise for the classification of tundra land cover since the polarimetric information is sensitive to low vegetation and the wetlands. Furthermore, co-polarized data provide a higher spatial resolution than the quad-polarized data.
The analysis of the intermediate digital elevation model data of the TanDEM-X showed a high potential for the characterization of the surface morphology. The basic and relative topographic features were shown to be of high relevance for the quantification of the surface morphology and an area-wide application is feasible. In addition, these data were of value for the classification and delineation of landforms. Such classifications will assist the delineation of geomorphological units and have potential to identify locations of actual and future morphologic activity.
Heat and excessive solar radiation can produce abiotic stresses during apple maturation, resulting fruit quality. Therefore, the monitoring of temperature on fruit surface (FST) over the growing period can allow to identify thresholds, above of which several physiological disorders such as sunburn may occur in apple.
The current approaches neglect spatial variation of FST and have reduced repeatability, resulting in unreliable predictions. In this study, LiDAR laser scanning and thermal imaging were employed to detect the temperature on fruit surface by means of 3D point cloud. A process for calibrating the two sensors based on an active board target and producing a 3D thermal point cloud was suggested. After calibration, the sensor system was utilised to scan the fruit trees, while temperature values assigned in the corresponding 3D point cloud were based on the extrinsic calibration. Whereas a fruit detection algorithm was performed to segment the FST from each apple.
• The approach allows the calibration of LiDAR laser scanner with thermal camera in order to produce a 3D thermal point cloud.
• The method can be applied in apple trees for segmenting FST in 3D. Whereas the approach can be utilised to predict several physiological disorders including sunburn on fruit surface.
In this paper, we bridge the gap between procedural content generation (PCG) and user-generated content (UGC) by proposing and demonstrating an interactive agent-based model of self-assembling ensembles that can be directed though user input. We motivate these efforts by considering the opportunities technology provides to pursue game designs based on according game design frameworks. We present three different use cases of the proposed model that emphasize its potential to (1) self-assemble into predefined 3D graphical assets, (2) define new structures in the context of virtual environments by self-assembling layers on the surfaces of arbitrary 3D objects, and (3) allow novel structures to self-assemble only considering the model’s configuration and no external dependencies. To address the performance restrictions in computer games, we realized the prototypical model implementation by means of an efficient entity component system (ECS). We conclude the paper with an outlook on future steps to further explore novel interactive, dynamic PCG mechanics and to ensure their efficiency.
This thesis is devoted to the study of computational complexity theory, a branch of theoretical computer science. Computational complexity theory investigates the inherent difficulty in designing efficient algorithms for computational problems. By doing so, it analyses the scalability of computational problems and algorithms and places practical limits on what computers can actually accomplish. Computational problems are categorised into complexity classes. Among the most important complexity classes are the class NP and the subclass of NP-complete problems, which comprises many important optimisation problems in the field of operations research. Moreover, with the P-NP-problem, the class NP represents the most important unsolved question in computer science. The first part of this thesis is devoted to the study of NP-complete-, and more generally, NP-hard problems. It aims at improving our understanding of this important complexity class by systematically studying how altering NP-hard sets affects their NP-hardness. This research is related to longstanding open questions concerning the complexity of unions of disjoint NP-complete sets, and the existence of sparse NP-hard sets. The second part of the thesis is also dedicated to complexity classes but takes a different perspective: In a sense, after investigating the interior of complexity classes in the first part, the focus shifts to the description of complexity classes and thereby to the exterior in the second part. It deals with the description of complexity classes through leaf languages, a uniform framework which allows us to characterise a great variety of important complexity classes. The known concepts are complemented by a new leaf-language model. To a certain extent, this new approach combines the advantages of the known models. The presented results give evidence that the connection between the theory of formal languages and computational complexity theory might be closer than formerly known.
Background
Information extraction techniques that get structured representations out of unstructured data make a large amount of clinically relevant information about patients accessible for semantic applications. These methods typically rely on standardized terminologies that guide this process. Many languages and clinical domains, however, lack appropriate resources and tools, as well as evaluations of their applications, especially if detailed conceptualizations of the domain are required. For instance, German transthoracic echocardiography reports have not been targeted sufficiently before, despite of their importance for clinical trials. This work therefore aimed at development and evaluation of an information extraction component with a fine-grained terminology that enables to recognize almost all relevant information stated in German transthoracic echocardiography reports at the University Hospital of Würzburg.
Methods
A domain expert validated and iteratively refined an automatically inferred base terminology. The terminology was used by an ontology-driven information extraction system that outputs attribute value pairs. The final component has been mapped to the central elements of a standardized terminology, and it has been evaluated according to documents with different layouts.
Results
The final system achieved state-of-the-art precision (micro average.996) and recall (micro average.961) on 100 test documents that represent more than 90 % of all reports. In particular, principal aspects as defined in a standardized external terminology were recognized with f 1=.989 (micro average) and f 1=.963 (macro average). As a result of keyword matching and restraint concept extraction, the system obtained high precision also on unstructured or exceptionally short documents, and documents with uncommon layout.
Conclusions
The developed terminology and the proposed information extraction system allow to extract fine-grained information from German semi-structured transthoracic echocardiography reports with very high precision and high recall on the majority of documents at the University Hospital of Würzburg. Extracted results populate a clinical data warehouse which supports clinical research.
Parametric weighted finite automata (PWFA) are a multi-dimensional generalization of weighted finite automata. The expressiveness of PWFA contains the expressiveness of weighted finite automata as well as the expressiveness of affine iterated function system. The thesis discusses theory and applications of PWFA. The properties of PWFA definable sets are studied and it is shown that some fractal generator systems can be simulated using PWFA and that various real and complex functions can be represented by PWFA. Furthermore, the decoding of PWFA and the interpretation of PWFA definable sets is discussed.
The issue of sustainability is at the top of the political and societal agenda, being considered of extreme importance and urgency. Human individual action impacts the environment both locally (e.g., local air/water quality, noise disturbance) and globally (e.g., climate change, resource use). Urban environments represent a crucial example, with an increasing realization that the most effective way of producing a change is involving the citizens themselves in monitoring campaigns (a citizen science bottom-up approach). This is possible by developing novel technologies and IT infrastructures enabling large citizen participation. Here, in the wider framework of one of the first such projects, we show results from an international competition where citizens were involved in mobile air pollution monitoring using low cost sensing devices, combined with a web-based game to monitor perceived levels of pollution. Measures of shift in perceptions over the course of the campaign are provided, together with insights into participatory patterns emerging from this study. Interesting effects related to inertia and to direct involvement in measurement activities rather than indirect information exposure are also highlighted, indicating that direct involvement can enhance learning and environmental awareness. In the future, this could result in better adoption of policies towards decreasing pollution.
Object six Degrees of Freedom (6DOF) pose estimation is a fundamental problem in many practical robotic applications, where the target or an obstacle with a simple or complex shape can move fast in cluttered environments. In this thesis, a 6DOF pose estimation algorithm is developed based on the fused data from a time-of-flight camera and a color camera. The algorithm is divided into two stages, an annealed particle filter based coarse pose estimation stage and a gradient decent based accurate pose optimization stage. In the first stage, each particle is evaluated with sparse representation. In this stage, the large inter-frame motion of the target can be well handled. In the second stage, the range data based conventional Iterative Closest Point is extended by incorporating the target appearance information and used for calculating the accurate pose by refining the coarse estimate from the first stage. For dealing with significant illumination variations during the tracking, spherical harmonic illumination modeling is investigated and integrated into both stages. The robustness and accuracy of the proposed algorithm are demonstrated through experiments on various objects in both indoor and outdoor environments. Moreover, real-time performance can be achieved with graphics processing unit acceleration.
In many real world settings, imbalanced data impedes model performance of learning algorithms, like neural networks, mostly for rare cases. This is especially problematic for tasks focusing on these rare occurrences. For example, when estimating precipitation, extreme rainfall events are scarce but important considering their potential consequences. While there are numerous well studied solutions for classification settings, most of them cannot be applied to regression easily. Of the few solutions for regression tasks, barely any have explored cost-sensitive learning which is known to have advantages compared to sampling-based methods in classification tasks. In this work, we propose a sample weighting approach for imbalanced regression datasets called DenseWeight and a cost-sensitive learning approach for neural network regression with imbalanced data called DenseLoss based on our weighting scheme. DenseWeight weights data points according to their target value rarities through kernel density estimation (KDE). DenseLoss adjusts each data point’s influence on the loss according to DenseWeight, giving rare data points more influence on model training compared to common data points. We show on multiple differently distributed datasets that DenseLoss significantly improves model performance for rare data points through its density-based weighting scheme. Additionally, we compare DenseLoss to the state-of-the-art method SMOGN, finding that our method mostly yields better performance. Our approach provides more control over model training as it enables us to actively decide on the trade-off between focusing on common or rare cases through a single hyperparameter, allowing the training of better models for rare data points.
Climate models are the tool of choice for scientists researching climate change. Like all models they suffer from errors, particularly systematic and location-specific representation errors. One way to reduce these errors is model output statistics (MOS) where the model output is fitted to observational data with machine learning. In this work, we assess the use of convolutional Deep Learning climate MOS approaches and present the ConvMOS architecture which is specifically designed based on the observation that there are systematic and location-specific errors in the precipitation estimates of climate models. We apply ConvMOS models to the simulated precipitation of the regional climate model REMO, showing that a combination of per-location model parameters for reducing location-specific errors and global model parameters for reducing systematic errors is indeed beneficial for MOS performance. We find that ConvMOS models can reduce errors considerably and perform significantly better than three commonly used MOS approaches and plain ResNet and U-Net models in most cases. Our results show that non-linear MOS models underestimate the number of extreme precipitation events, which we alleviate by training models specialized towards extreme precipitation events with the imbalanced regression method DenseLoss. While we consider climate MOS, we argue that aspects of ConvMOS may also be beneficial in other domains with geospatial data, such as air pollution modeling or weather forecasts.
Virtual environments (VEs) can evoke and support emotions, as experienced when playing emotionally arousing games. We theoretically approach the design of fear and joy evoking VEs based on a literature review of empirical studies on virtual and real environments as well as video games’ reviews and content analyses. We define the design space and identify central design elements that evoke specific positive and negative emotions. Based on that, we derive and present guidelines for emotion-inducing VE design with respect to design themes, colors and textures, and lighting configurations. To validate our guidelines in two user studies, we 1) expose participants to 360° videos of VEs designed following the individual guidelines and 2) immerse them in a neutral, positive and negative emotion-inducing VEs combining all respective guidelines in Virtual Reality. The results support our theoretically derived guidelines by revealing significant differences in terms of fear and joy induction.
Recently, several classifiers that combine primary tumor data, like gene expression data, and secondary data sources, such as protein-protein interaction networks, have been proposed for predicting outcome in breast cancer. In these approaches, new composite features are typically constructed by aggregating the expression levels of several genes. The secondary data sources are employed to guide this aggregation. Although many studies claim that these approaches improve classification performance over single genes classifiers, the gain in performance is difficult to assess. This stems mainly from the fact that different breast cancer data sets and validation procedures are employed to assess the performance. Here we address these issues by employing a large cohort of six breast cancer data sets as benchmark set and by performing an unbiased evaluation of the classification accuracies of the different approaches. Contrary to previous claims, we find that composite feature classifiers do not outperform simple single genes classifiers. We investigate the effect of (1) the number of selected features; (2) the specific gene set from which features are selected; (3) the size of the training set and (4) the heterogeneity of the data set on the performance of composite feature and single genes classifiers. Strikingly, we find that randomization of secondary data sources, which destroys all biological information in these sources, does not result in a deterioration in performance of composite feature classifiers. Finally, we show that when a proper correction for gene set size is performed, the stability of single genes sets is similar to the stability of composite feature sets. Based on these results there is currently no reason to prefer prognostic classifiers based on composite features over single genes classifiers for predicting outcome in breast cancer.
In the future Internet, the people-centric communication paradigm will be complemented by a ubiquitous communication among people and devices, or even a communication between devices. This comes along with the need for a more flexible, cheap, widely available Internet access. Two types of wireless networks are considered most appropriate for attaining those goals. While wireless sensor networks (WSNs) enhance the Internet’s reach by providing data about the properties of the environment, wireless mesh networks (WMNs) extend the Internet access possibilities beyond the wired backbone. This monograph contains four chapters which present modeling and optimization methods for WSNs and WMNs. Minimizing energy consumptions is the most important goal of WSN optimization and the literature consequently provides countless energy consumption models. The first part of the monograph studies to what extent the used energy consumption model influences the outcome of analytical WSN optimizations. These considerations enable the second contribution, namely overcoming the problems on the way to a standardized energy-efficient WSN communication stack based on IEEE 802.15.4 and ZigBee. For WMNs both problems are of minor interest whereas the network performance has a higher weight. The third part of the work, therefore, presents algorithms for calculating the max-min fair network throughput in WMNs with multiple link rates and Internet gateway. The last contribution of the monograph investigates the impact of the LRA concept which proposes to systematically assign more robust link rates than actually necessary, thereby allowing to exploit the trade-off between spatial reuse and per-link throughput. A systematical study shows that a network-wide slightly more conservative LRA than necessary increases the throughput of a WMN where max-min fairness is guaranteed. It moreover turns out that LRA is suitable for increasing the performance of a contention-based WMN and is a valuable optimization tool.
We consider competitive location problems where two competing providers place their facilities sequentially and users can decide between the competitors. We assume that both competitors act non-cooperatively and aim at maximizing their own benefits. We investigate the complexity and approximability of such problems on graphs, in particular on simple graph classes such as trees and paths. We also develop fast algorithms for single competitive location problems where each provider places a single facilty. Voting location, in contrast, aims at identifying locations that meet social criteria. The provider wants to satisfy the users (customers) of the facility to be opened. In general, there is no location that is favored by all users. Therefore, a satisfactory compromise has to be found. To this end, criteria arising from voting theory are considered. The solution of the location problem is understood as the winner of a virtual election among the users of the facilities, in which the potential locations play the role of the candidates and the users represent the voters. Competitive and voting location problems turn out to be closely related.
The holy grail of structural biology is to study a protein in situ, and this goal has been fast approaching since the resolution revolution and the achievement of atomic resolution. A cell's interior is not a dilute environment, and proteins have evolved to fold and function as needed in that environment; as such, an investigation of a cellular component should ideally include the full complexity of the cellular environment. Imaging whole cells in three dimensions using electron cryotomography is the best method to accomplish this goal, but it comes with a limitation on sample thickness and produces noisy data unamenable to direct analysis. This thesis establishes a novel workflow to systematically analyse whole-cell electron cryotomography data in three dimensions and to find and identify instances of protein complexes in the data to set up a determination of their structure and identity for success. Mycoplasma pneumoniae is a very small parasitic bacterium with fewer than 700 protein-coding genes, is thin enough and small enough to be imaged in large quantities by electron cryotomography, and can grow directly on the grids used for imaging, making it ideal for exploratory studies in structural proteomics. As part of the workflow, a methodology for training deep-learning-based particle-picking models is established.
As a proof of principle, a dataset of whole-cell Mycoplasma pneumoniae tomograms is used with this workflow to characterize a novel membrane-associated complex observed in the data. Ultimately, 25431 such particles are picked from 353 tomograms and refined to a density map with a resolution of 11 Å. Making good use of orthogonal datasets to filter search space and verify results, structures were predicted for candidate proteins and checked for suitable fit in the density map. In the end, with this approach, nine proteins were found to be part of the complex, which appears to be associated with chaperone activity and interact with translocon machinery.
Visual proteomics refers to the ultimate potential of in situ electron cryotomography: the comprehensive interpretation of tomograms. The workflow presented here is demonstrated to help in reaching that potential.
Studies investigating the correlates of immune protection against Yersinia infection have established that both humoral and cell mediated immune responses are required for the comprehensive protection. In our previous study, we established that the bivalent fusion protein (rVE) comprising immunologically active regions of Y pestis LcrV (100-270 aa) and YopE (50-213 aa) proteins conferred complete passive and active protection against lethal Y enterocolitica 8081 challenge. In the present study, cohort of BALB/c mice immunized with rVE or its component proteins rV, rE were assessed for cell mediated immune responses and memory immune protection against Y enterocolitica 8081 rVE immunization resulted in extensive proliferation of both CD4 and CD8 T cell subsets; significantly high antibody titer with balanced IgG1: IgG2a/IgG2b isotypes (1:1 ratio) and up regulation of both Th1 (INF-\(\alpha\), IFN-\(\gamma\), IL 2, and IL 12) and Th2 (IL 4) cytokines. On the other hand, rV immunization resulted in Th2 biased IgG response (11:1 ratio) and proliferation of CD4+ T-cell; rE group of mice exhibited considerably lower serum antibody titer with predominant Th1 response (1:3 ratio) and CD8+ T-cell proliferation. Comprehensive protection with superior survival (100%) was observed among rVE immunized mice when compared to the significantly lower survival rates among rE (37.5%) and rV (25%) groups when IP challenged with Y enterocolitica 8081 after 120 days of immunization. Findings in this and our earlier studies define the bivalent fusion protein rVE as a potent candidate vaccine molecule with the capability to concurrently stimulate humoral and cell mediated immune responses and a proof of concept for developing efficient subunit vaccines against Gram negative facultative intracellular bacterial pathogens.
State Management at line rate is crucial for critical applications in next-generation networks. P4 is a language used in software-defined networking to program the data plane. The data plane can profit in many circumstances when it is allowed to manage its state without any detour over a controller. This work is based on a previous study by investigating the potential and performance of add-on-miss insertions of state by the data plane. The state keeping capabilities of P4 are limited regarding the amount of data and the update frequency. We follow the tentative specification of an upcoming portable-NIC-architecture and implement these changes into the software P4 target T4P4S. We show that insertions are possible with only a slight overhead compared to lookups and evaluate the influence of the rate of insertions on their latency.
To deliver the best user experience (UX), the human-centered design cycle (HCDC) serves as a well-established guideline to application developers. However, it does not yet cover network-specific requirements, which become increasingly crucial, as most applications deliver experience over the Internet. The missing network-centric view is provided by Quality of Experience (QoE), which could team up with UX towards an improved overall experience. By considering QoE aspects during the development process, it can be achieved that applications become network-aware by design. In this paper, the Quality of Experience Centered Design Cycle (QoE-CDC) is proposed, which provides guidelines on how to design applications with respect to network-specific requirements and QoE. Its practical value is showcased for popular application types and validated by outlining the design of a new smartphone application. We show that combining HCDC and QoE-CDC will result in an application design, which reaches a high UX and avoids QoE degradation.