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Objectives: Crayfish plague disease, caused by the oomycete pathogen Aphanomyces astaci represents one of the greatest risks for the biodiversity of the freshwater crayfish. This data article covers the de novo transcriptome assembly and annotation data of the noble crayfish and the marbled crayfish challenged with Ap. astaci. Following the controlled infection experiment (Francesconi et al. in Front Ecol Evol, 2021, https://doi.org/10.3389/fevo.2021.647037), we conducted a differential gene expression analysis described in (Boštjančić et al. in BMC Genom, 2022, https://doi.org/10.1186/s12864-022-08571-z) Data description: In total, 25 noble crayfish and 30 marbled crayfish were selected. Hepatopancreas tissue was isolated, followed by RNA sequencing using the Illumina NovaSeq 6000 platform. Raw data was checked for quality with FastQC, adapter and quality trimming were conducted using Trimmomatic followed by de novo assembly with Trinity. Assembly quality was assessed with BUSCO, at 93.30% and 93.98% completeness for the noble crayfish and the marbled crayfish, respectively. Transcripts were annotated using the Dammit! pipeline and assigned to KEGG pathways. Respective transcriptome and raw datasets may be reused as the reference transcriptome assemblies for future expression studies.
This thesis explores a 3D object detection and pose estimation approach based on the point pair features method presented by Drost et. al. [Dro+10]. While pose estimation methods have shown good improvements, they still remain a crucial problem on the computer vision field. In this work, we implemented a program that takes point cloud scenes as input and returns the detected object with their estimated pose. The program fully covers an object detection pipeline by processing 3D models during an offline phase, extracting their point pair features and creating a global descriptor out of them. During an online phase, the same features are extracted from a point cloud scene and are matched to the model features. After the voting scheme, potential poses of the object are retrieved. The poses end being clustered together and post-processed to finally deliver a result. The program was tested using simulated and real data. We evaluate these tests and present the final results, by discussing the achieved accuracy of the detections and the estimated poses.
The decline of biodiversity can be observed worldwide and its consequences are alarming. It is therefore crucial that nature must be protected and, where possible, restored. A wide variety of different project options are possible. Yet in the context of limited availability of resources, the selection of the most efficient measures is increasingly important. For this purpose, there is still a lack of information. This pertains, as outlined in the next paragraph, in particular, to information at different scales of projects.
Firstly, there is a lack of information on the concrete added value of biodiversity protection projects. Secondly, there is a lack of information on the actual impacts of such projects and on the costs and benefits associated with a project. Finally, there is a lack of information on the links between the design of a project, the associated framework conditions and the perception of specific impacts. This paper addresses this knowledge gap by providing more information on the three scales by means of three empirical studies on three different biodiversity protection projects in order to help optimize future projects.
The first study “Assessing the trade-offs in more nature-friendly mosquito control in the Upper Rhine region” examines the added value of a more nature-friendly mosquito control in the Upper Rhine Valley of Germany using a contingent valuation method. Recent studies show that the widely used biocide Bti, which is used as the main mosquito control agent in many parts of the world, has more negative effects on nature than previously expected. However, it is not yet clear whether the population supports a more nature-friendly mosquito control, as such an adaptation could potentially lead to higher nuisance. This study attempts to answer this question by assessing the willingness to pay for an adapted mosquito control strategy that reduces the use of Bti, while maintaining nuisance protection within settlements. The results show that the majority of the surveyed population attaches a high value to a more nature-friendly mosquito control and is willing to accept a higher nuisance outside of the villages.
The second study “Inner city river restoration projects: the role of project components for acceptance” examines the acceptance of a river restoration project in Rhineland-Palatinate, Germany. Despite much effort, many rivers worldwide are still in poor condition. Therefore, a rapid implementation of river restoration projects is of great importance. In this context, acceptance by society plays a fundamental role, however, the factors determining such acceptance are still poorly understood. In particular, the complex interplay between the acceptance or rejection of specific project components and the acceptance of the overall project require further exploration. This study addresses this knowledge gap by assessing the acceptance of the project, its various ecological and social components, and the perception of real and fictitious costs as well as the benefits of the components. Our findings demonstrate that while acceptance of the overall project is generally rather high, many respondents reject one or more of the project's components. Complementary social project components, like a playground, find less support than purely ecological components. Overall, our research shows that complementary components may increase or decrease acceptance of the overall project. We, furthermore, found that differences in the acceptance of the individual components depend on individual concerns, such as perceived flood risk, construction costs, expected noise and littering as well as the quality of communication, attachment to the site, and the age of the respondents.
The third study “What determines preferences for semi-natural habitats in agrarian landscapes? A choice-modelling approach across two countries using attributes characterizing vegetation” investigates people's aesthetic preferences for semi-natural habitats in agricultural landscapes. The EU-Common Agricultural Policy promotes the introduction of woody and grassy semi-natural habitats (SNH) in agricultural landscapes. While the benefits of these structures in terms of regulating ecosystem services are already well understood, the effects of SNH on visual landscape quality is still not clear. This study investigates the factors determining people’s visual preferences in the context of grassy and woody SNH elements in Swiss and Hungarian landscapes using picture-based choice experiments. The results suggest that respondents’ choices strongly depend on specific vegetation characteristics that appear and disappear over the year. In particular, flowers as a source of colours and green vegetation as well as ordered structure and the proportion of uncovered soil in the picture play an important role regarding respondents’ aesthetic perceptions of the pictures.
The three empirical studies can help to make future projects in the study areas of biodiversity protection more efficient. While this thesis highlights the importance of exploring biodiversity protection projects at different scales, further analyses of the different scales of biodiversity protection projects are needed to provide a sound basis to develop guidance on identifying the most efficient biodiversity protection projects.
Instructor feedback on written assignments is one of the most important elements in the writing process, especially for students writing in English as a foreign language. However, students are often critical of both the amount and quality of the feedback they receive. In order to better understand what makes feedback effective, this study explored the nature of students’ assessments of the educational alliance, and how their receptivity to, perceptions of, and decisions about using their instructors’ feedback differed depending on how strong they believed the educational alliance to be. This exploratory case study found that students not only assessed the quality of the educational alliance based on goal compatibility, task relevance, and teacher effectiveness, but that there was also a reciprocal relationship between these elements. Furthermore, students’ perceptions of the educational alliance directly influenced how they perceived the feedback, which made the instructor’s choice of feedback method largely irrelevant. Stronger educational alliances resulted in higher instances of critical engagement, intrinsic motivation, and feelings of self-efficacy. The multidirectional influence of goal, task, and bond mean that instructors who want to maximize their feedback efforts need to attend to all three.
Social networks are ubiquitous structures that we generate and enrich every-day while connecting with people through social media platforms, emails, and any other type of interaction. While these structures are intangible to us, they carry important information. For instance, the political leaning of our friends can be a proxy to identify our own political preferences. Similarly, the credit score of our friends can be decisive in the approval or rejection of our own loans. This explanatory power is being leveraged in public policy, business decision-making and scientific research because it helps machine learning techniques to make accurate predictions. However, these generalizations often benefit the majority of people who shape the general structure of the network, and put in disadvantage under-represented groups by limiting their resources and opportunities. Therefore it is crucial to first understand how social networks form to then verify to what extent their mechanisms of edge formation contribute to reinforce social inequalities in machine learning algorithms.
To this end, in the first part of this thesis, I propose HopRank and Janus two methods to characterize the mechanisms of edge formation in real-world undirected social networks. HopRank is a model of information foraging on networks. Its key component is a biased random walker based on transition probabilities between k-hop neighborhoods. Janus is a Bayesian framework that allows to identify and rank plausible hypotheses of edge formation in cases where nodes possess additional information. In the second part of this thesis, I investigate the implications of these mechanisms - that explain edge formation in social networks - on machine learning. Specifically, I study the influence of homophily, preferential attachment, edge density, fraction of inorities, and the directionality of links on both performance and bias of collective classification, and on the visibility of minorities in top-k ranks. My findings demonstrate a strong correlation between network structure and machine learning outcomes. This suggests that systematic discrimination against certain people can be: (i) anticipated by the type of network, and (ii) mitigated by connecting strategically in the network.
In this thesis the possibilities for real-time visualization of OpenVDB
files are investigated. The basics of OpenVDB, its possibilities, as well
as NanoVDB and its GPU port, were studied. A system was developed
using PNanoVDB, the graphics API port of OpenVDB. Techniques were
explored to improve and accelerate a single ray approach of ray tracing.
To prove real-time capability, two single scattering approaches were
also implemented. One of these was selected, further investigated and
optimized to achieve interactive real-time rendering.
It is important to give artists immediate feedback on their adjustments, as
well as the possibility to change all parameters to ensure a user friendly
creation process.
In addition to the optical rendering, corresponding benchmarks were
collected to compare different improvement approaches and to prove
their relevance. Attention was paid to the rendering times and memory
consumption on the GPU to ensure optimal use. A special focus, when
rendering OpenVDB files, was put on the integrability and extensibility of
the program to allow easy integration into an existing real-time renderer
like U-Render.
Semantic Web technologies have been recognized to be key for the integration of distributed and heterogeneous data sources on the Web, as they provide means to define typed links between resources in a dynamic manner and following the principles of dataspaces. The widespread adoption of these technologies in the last years led to a large volume and variety of data sets published as machine-readable RDF data, that once linked constitute the so-called Web of Data. Given the large scale of the data, these links are typically generated by computational methods that given a set of RDF data sets, analyze their content and identify the entities and schema elements that should be connected via the links. Analogously to any other kind of data, in order to be truly useful and ready to be consumed, links need to comply with the criteria of high quality data (e.g., syntactically and semantically accurate, consistent, up-to-date). Despite the progress in the field of machine learning, human intelligence is still essential in the quest for high quality links: humans can train algorithms by labeling reference examples, validate the output of algorithms to verify their performance on a data set basis, as well as augment the resulting set of links. Humans —especially expert humans, however, have limited availability. Hence, extending data quality management processes from data owners/publishers to a broader audience can significantly improve the data quality management life cycle.
Recent advances in human computation and peer-production technologies opened new avenues for human-machine data management techniques, allowing to involve non-experts in certain tasks and providing methods for cooperative approaches. The research work presented in this thesis takes advantage of such technologies and investigates human-machine methods that aim at facilitating link quality management in the Semantic Web. Firstly, and focusing on the dimension of link accuracy, a method for crowdsourcing ontology alignment is presented. This method, also applicable to entities, is implemented as a complement to automatic ontology alignment algorithms. Secondly, novel measures for the dimension of information gain facilitated by the links are introduced. These entropy-centric measures provide data managers with information about the extent the entities in the linked data set gain information in terms of entity description, connectivity and schema heterogeneity. Thirdly, taking Wikidata —the most successful case of a linked data set curated, linked and maintained by a community of humans and bots— as a case study, we apply descriptive and predictive data mining techniques to study participation inequality and user attrition. Our findings and method can help community managers make decisions on when/how to intervene with user retention plans. Lastly, an ontology to model the history of crowd contributions across marketplaces is presented. While the field of human-machine data management poses complex social and technical challenges, the work in this thesis aims to contribute to the development of this still emerging field.
The presented study was motivated by the dynamic phenomena observed in basic catalytic surface reactions, especially by bi- and tristability, and the interactions between these stable states. In this regard, three reaction-diffusion models were developed and examined using bifurcation theory and numerical simulations.
A first model was designed to extend the bistable CO oxidation on Ir(111) to include hydrogen and its oxidation. The differential equation system was analyzed within the framework of bifurcation theory, revealing three branches of stable solutions.
One state is characterized by high formation rates (upper rate state, UR), while the other two branches display low formation rates (lower rate (LR) \& very low rate (VLR) states).
The overlapping branches form the shape of a `swallowtail', the curve of saddle-node bifurcations forming two cusps. Increasing the temperature leads to a subsequent unfolding and hence decreases the system complexity.
A series of numerical simulations representing possible experiments was conducted to illustrate the experimental accessibility (or the lack) of said states. Relaxation experiments show partially long decay times. Quasistatic scanning illustrates the existence of all three states within the tristable regime and their respective conversion once crossing a fold.
A first attempt regarding the state dominance in reaction-diffusion fronts was done. While UR seems to dominate in 1D, a 2D time-evolution shows that LR invades the interphase between UR and VLR.
Subsequently, a generic monospecies mock model was used for the comprehensive study of reaction-diffusion fronts. A quintic polynomial as reaction term was chosen, derived by the sixth-order potential associated with the `butterfly bifurcation'. This ensures up to three stable solutions($u_{0}$,$u_{1}$,$u_{2}$), depending on the four-dimensional parameter space.
The model was explored extensively, identifying regions with similar behaviors.
A term for the front velocity connecting two stable states was derived, depending only on the relative difference of the states' potential wells.
Equipotential curves were found, where the front velocity vanishes of a given front. Numerical simulations on a two-dimensional, finite disk using a triangulated mesh supported these findings.
Additionally, the front-splitting instability was observed for certain parameters. The front solution $u_{02}$ becomes unstable and divides into $u_{01}$ and $u_{12}$, exhibiting different front velocities. A good estimate for the limit of the front splitting region was given and tested using time evolutions.
Finally, the established mock model was modified from continuous to discrete space, utilizing a simple domain in 1D and three different lattices in 2D (square, hexagonal, triangular).
For low diffusivities or large distances between coupling nodes, fronts can become pinned, if the parameters are within range of the equipotential lines. This phenomenon is known as propagation failure and its extent in parameter space was explored in 1D. In 2D, an estimate was given for remarkable front orientations respective to the lattice using a pseudo-2D approximation. Near the pinning region, front velocities differ significantly from the continuous expectation as the shape of the curve potential becomes significant. Factors that decide the size and shape of the pinning regions are the coupling strength, the lattice, the front orientation relative to the lattice, and the front itself. The bifurcation diagram shows a snaking curve in the pinning region, each alternating branch representing a stable or unstable frozen front solution. Numerical simulations supported the observations concerning propagation failure and lattice dependence.
Furthermore, the influence of front orientation on the front velocity was explored in greater detail, showing that fronts with certain lattice-dependent orientations are more or less prone to propagation failure. This leads to the possibility of pattern formation, reflecting the lattice geometry. An attempt to quantify the front movement depending on angular front orientation has shown reasonable results and good agreement with the pseudo-2D approach.
The growing numbers of breeding rooks (Corvus frugilegus) in the city of Landau (Rhineland- Palatinate, Germany) increase the potential for conflict between rooks and humans, which is mainly associated with noise and faeces. Therefore, the aim of this work is a better understanding of the breeding tree selection of the rook in order to develop options for action and management in the future.
Part I of this thesis provides general background information on the rook and includes mapping of the rookeries in the Anterior Palatinate and South Palatinate including Landau in the year 2020. That mapping revealed that the number of rural colonies has decreased, while the number of urban colonies has increased in the study area in the last few years. In line with current literature, tree species and tree size were important criteria for breeding tree selection. However, the mapping showed that additional factors must be important as well.
Therefore, as rooks seem to often breed along traffic axes, Part II of this thesis examines how temperature, artificial light and noise, which are all linked to traffic axes, affect the breeding tree selection of the rook in the city of Landau. The following three hypotheses are developed: (1) manually selected breeding trees (Bm) have a warmer microclimate than manually selected non-breeding trees (Nm) or randomly selected non-breeding trees (Nr), (2) Bm are exposed to a higher light level than Nm or Nr and (3) Bm are exposed to a higher noise level than Nm or Nr. To test these hypotheses, 15 Bm, 13 Nm and 16 Nr are investigated.
The results show that Bm were exposed to more noise than both types of non-breeding trees (μBm, noise = 36.52481 dB, μNm, noise = 31.27229 dB, μNr, noise = 29.17417 dB) where the difference between Bm and Nr was significant. In addition, there was a tendency for Bm to be exposed to less light (μBm, light = 0.356 lx) than Nm (μNm, light = 0.4107692 lx) and significantly less light than Nr (μNr, light = 1.995 lx), while temperature did not differ between the groups (μBm, temp = 16.90549 °C, μNm, temp = 16.93118 °C, μNr, temp = 17.28639 °C).
This study shows for the first time that rooks prefer trees which are exposed to low light levels and high noise levels, i.e. more intense traffic noise, for breeding. It can only be speculated that the cause of this is lower enemy pressure at such sites. The fact that temperature does not seem to have any influence on breeding tree selection may be due to only small temperature differences at nest height, which might be compensated by breeding behaviour. Consequently, in the long term one management approach could be to divert traffic from inner-city areas, especially schools and hospitals, to bypasses. If tree genera suitable for rooks, such as plane trees, are planted along the bypasses, those sites could provide suitable alternative habitats to inner-city breeding locations, which become less attractive for breeding due to noise reduction. In the short term in addition to locally implemented repellent measures the most effective approach is to strengthen rook acceptance among the population. However, further research is needed to verify the results of this thesis and to gain further insights into rook breeding site selection in order to develop effective management measures.
Background. Agricultural plastic mulches offer great benefits such as higher yields and lower pesticide use. Yet, plastic mulches may disintegrate over time and fragment into smaller debris. Such plastic debris is expected to remain in the field after removal of the plastic mulch and thus contributes to soil contamination with plastics.
Method. To investigate this, we collected soil samples at 0–10 cm and 10–40 cm depth from three fields covered with black mulch film for three consecutive years. Three fields without any reported plastic use served as control. Visual plastic debris > 1 cm (macroplastics) was collected from the soil surface. Mesoplastics between 2 mm and 1 cm were density separated from the sampled soil using saturated NaCl solution and analyzed by Fourier-transform infrared spectroscopy. Debris ≤ 2 mm (microplastics) was dispersed from 50 g soil using sodium hexametaphosphate solution followed by the aforementioned density separation. The separated polyethylene (PE), polypropylene (PP), and polystyrene (PS) were quantified via solvent-based pyrolysis–gas chromatography/mass spectrometry (Py–GC/MS).
Results. With 89–206 fragments ha−1, the majority of macroplastics were located in fields previously covered with mulch films. 80% of the collected specimen were identified as black PE film. The number of mesoplastics in plastic-mulched soil was 2.3 particles kg−1, while only 1.0 particles kg−1 were found in the reference fields. Py–GC/MS revealed microplastic levels of up to 13 mg kg−1. The PE content was significantly higher in plastic-mulched fields than in reference fields.
Discussion. Although the identified plastic levels are lower than those reported in comparable studies, our results still suggest that plastic mulching functions as a source of plastic debris in agricultural systems. Due to its severely restricted degradability, these plastics are likely to accumulate in soil in the long term and further fragment into smaller and smaller debris.