Site-Search Process for Synaptic Protein-DNA Complexes

The assembly of synaptic protein-DNA complexes by specialized proteins is critical for bringing together two distant sites within a DNA molecule or bridging two DNA molecules. The assembly of such synaptosomes is needed in numerous genetic processes requiring the interactions of two or more sites. The molecular mechanisms by which the protein brings the sites together, enabling the assembly of synaptosomes, remain unknown. Such proteins can utilize sliding, jumping, and segmental transfer pathways proposed for the single-site search process, but none of these pathways explains how the synaptosome assembles. Here we used restriction enzyme SfiI, that requires the assembly of synaptosome for DNA cleavage, as our experimental system and applied time-lapse, high-speed AFM (HS-AFM) to directly visualize the site search process accomplished by the SfiI enzyme. For the single-site SfiI-DNA complexes, we were able to directly visualize such pathways as sliding, jumping, and segmental site transfer. However, within the synaptic looped complexes, we visualized the threading and site-bound segment transfer as the synaptosome-specific search pathways for SfiI. In addition, we visualised sliding and jumping pathways for the loop dissociated complexes. Based on our data, we propose the site-search model for synaptic protein-DNA systems.

From a hard nuclear state towards a soft nuclear repository state – participation, co-designing, learning and reversibility in the site selection process for a nuclear waste repository

Since 2013 the site search for a repository for highly radioactive waste has been taking place in Germany within the framework of a new governance architecture and under new political guidelines. Based on experiences with nuclear politics in the past, Jungk (1977) coined the term hard nuclear state, characterized by decisions made in a top-down manner. The Decide-Announce-Defend (DAD) strategy, which branded the nuclear state at that time, led to conflicts, mistrust of authorities and blockages. In particular, massive resistance developed against the planned final repository site at Gorleben. Nowadays, after more than 60 years deploying nuclear energy, the (energy) political balance of power has fundamentally changed. Parts of the anti-nuclear movement have been integrated into the political party system and have contributed significantly to the nuclear phase-out. In the course of this, the unfinished task of final disposal has been readdressed: with the Repository Site Selection Act (StandAG, 2017), which was passed in 2013 and amended in 2017, an ongoing process of public participation is stated. The site selection process is required to be learning, self-questioning, science-based, reversible, and participatory. The StandAG § 5 not only provides a basis for a fundamental dialogue between the regulator, the operator, and the public, but also for „co-design“ by common citizens. The StandAG considers various elements from different participation-friendly theories of democracy as well as specific governance concepts, which we refer to collectively as the soft nuclear repository state (cf. Brunnengräber, 2021). Its characteristics need to be worked out, as the StandAG only provides some indications, but no criteria, for what good and sufficient participation in the site selection process means and what its conditions for success should be. Based on preliminary considerations on democratic theory and governance aspects (part 1), we present what good participation could mean in the current procedure and what the framework conditions for good participation could be (part 2). Additionally, we present main findings from participatory observations from the ongoing site search process and identify conditions and indications of a successful future participation process based on the ongoing process (part 3). In the résumé, we turn to the question of which of the democracy-theoretical elements of the soft repository state are already recognizable in the present procedure, but also whether the current procedure provides additional indications towards the soft nuclear repository state (part 4).

Multiple evidence combination for web site search using server log analysis

In this thesis, a novel method is proposed to improve the retrieval performance by using web server logs. Web server logs are grouped into different sessions and then terms are extracted for each page in the session, meanwhile weights of terms are calculated. A new representation of web page from user's perspective is generated after going through the entire log. The new representation and the anchor-based representation are combined with original text-based representation. Two combination methods: combination of document representations and combination of ranking scores are investigated. In the experiments, three measurements are employed to evaluate the performance and the results show that for Cosine Similarity model, the highest improvement on top-10 precision is around 38%, for Okapi model, the hightest improvement is around 13%, for TFIDF model, the highest improvement is around 48% and for Indri model, the highest improvement is around 17%.

Multiple evidence combination for web site search using server log analysis

In this thesis, a novel method is proposed to improve the retrieval performance by using web server logs. Web server logs are grouped into different sessions and then terms are extracted for each page in the session, meanwhile weights of terms are calculated. A new representation of web page from user's perspective is generated after going through the entire log. The new representation and the anchor-based representation are combined with original text-based representation. Two combination methods: combination of document representations and combination of ranking scores are investigated. In the experiments, three measurements are employed to evaluate the performance and the results show that for Cosine Similarity model, the highest improvement on top-10 precision is around 38%, for Okapi model, the hightest improvement is around 13%, for TFIDF model, the highest improvement is around 48% and for Indri model, the highest improvement is around 17%.

Honey Bees Extract Map Coordinates from the Dance

Honeybees communicate locations by the waggle dance, a symbolic form of information transfer. Here we ask whether the recruited bee uses only the indicated course vector or translates it into a location vector on a cognitive map. Recruits were captured on exiting the hive and displaced to distant release sites. Their flights were tracked by radar. Both the vector portions of their flights and the ensuing tortuous search portions were strongly and differentially affected by release site. Search patterns were biased toward the true location of the food and away from the location given by adding release-site displacement to the danced vector. The results imply that the bees recruited by the dance access the indicated location of the food on a shared spatial representation. Thus, the bee dance communicates two messages, a flying instruction and a map location.

Website optimization for mobile devices

The results of a research on the optimization of the site of the Central Scientific Agricultural Library for mobile devices are presented. A historical overview of the development of ‘mobile’ sites is given, various approaches to their creation are discussed. Specifications of various mobile devices, their features, methods for determining the fact of switching a user from a mobile version to a version for a personal computer and means for determining the characteristics of a particular device are analyzed. The changes in the process of adaptation for mobile devices of various sections of the library's website are revealed: the main site, search interfaces of databases, reference books, encyclopedias, and electronic libraries.