Affektive Dimensionen von Forschungsdaten, ihrer Nachnutzung und Verwaltung

In diesem Working Paper möchte ich die Zusammenhänge zwischen Forschungsdaten, Datenmanagement und Affektivität unter mehreren Gesichtspunkten beleuchten. Zuallererst werde ich mich den Forschungsdaten und ihrem affektiven Gehalt widmen. Dies ist sowohl im Hinblick auf die Abbildung von Affekten in den Daten als auch in der Dokumentation der Forschung relevant. Ich werde nachfolgend anhand von Beispielen der Datenerhebung und der Sekundäranalyse erläutern, welche Dimensionen affektiver Dynamiken berücksichtigt werden können. Meine Ausführungen stützen sich auf ethnographische Forschungsdaten, da diese von ihrer Dichte und Vielfalt her die komplexen affektiven Prozesse in der Datenerzeugung und -auswertung besonders gut veranschaulichen können. Im zweiten Teil dieses Aufsatzes widme ich mich den Affekten der Forschenden, wenn es um die Verwaltung, Archivierung und Bereitstellung ihrer Daten geht. Die Verwendung der Begriffe Affekt und Affektivität lehnt sich an die im SFB 1171 Affective Societies erarbeiteten Definitionen an. Affektivität verstehe ich demnach als relationalen und dynamischen Prozess des Affizierens und Affiziertwerdens, der sich auf Individuen, Kollektive oder auch nichtmenschliche Körper beziehen kann (vgl. Slaby & Mühlhoff 2019)

The schlafen core domain: from structure to function

The immune system is a complex network of processes and structures to protect the organism against infectious diseases. All processes, which include the maturation of individual immune cells, must be strictly regulated to prevent malfunction. The schlafen protein family was recently reported to play key regulatory roles in T cell maturation and different subsets of individual schlafen family members are gradually upregulated during T cell maturation. The schlafen family belongs to the interferon-stimulated genes and various members play important roles in a plethora of cellular processes: regulation of the cell cycle, T cell quiescence, differentiation and proliferation of various cell types, tumorigenesis and inhibition of viral replication. All schlafen protein family members share the schlafen core domain, which is a highly conserved N- terminal region of approximately 340 amino acids. Based on sequence similarities, this region has been predicted to contain a divergent ATPase domain. Additionally, the longer schlafen protein members harbor a C-terminal domain with sequence homologies to superfamily 1 DNA/RNA helicases. Although the individual schlafen members play key roles in diverse cellular processes, they are poorly characterized in vitro and the underlying molecular mechanisms remain unknown. Since neither biochemical nor structural information were available, the overall goal of this study was to biochemically and structurally describe the schlafen proteins, and specifically their highly conserved schlafen core domain. Crystallographic studies performed during this thesis, revealed the structures of full length murine Schlafen 2 (Slfn2) and N-terminal human Schlafen 5 (SLFN51-336), which is the first high resolution structure of a human schlafen protein ever reported. Both crystal structures show a unique horseshoe shape with a novel fold harboring a highly conserved zinc finger. Interestingly, the schlafen core domain resembles no ATPase like fold and indeed, neither ATP-binding nor hydrolysis could be verified experimentally. Thus, structural information combined with experimental data prove that the schlafen core is no ATPase domain. Biochemical characterization discovered nucleic acid binding properties of the schlafen core domain. Binding affinities of SLFN51-336 increased in a length dependent manner for both, single-stranded DNA and RNA, although no preference for DNA or RNA could be identified. The highest affinity towards RNA was detected for a stem-loop structure and no binding for a RNA duplex, indicating that single-stranded regions are necessary for the interaction. The highest affinity of SLFN51-336 was measured with double-stranded DNA and the residues identified to be responsible for DNA binding were mapped to the zinc finger region by generating DNA-binding deficient mutants. Slfn2 was capable to bind both, DNA and RNA, with a 10 times higher affinity for both substrates than SLFN51-336. The 5S rRNA was identified by co-purification with Slfn2 as a potential nucleic acid substrate. Further biochemical investigations discovered a new function for SLFN51-336 and Slfn2, which is a 3’- 5’ exonuclease activity on single-stranded DNA in a metal ion-dependent, but ATP-independent manner. The importance of three conserved sites for DNA hydrolysis was confirmed by generating exonuclease-inactive mutants. However, the cleavage mechanism is not entirely solved and therefore a co-crystal structure of a substrate bound schlafen core domain would be of great benefit. Besides investigations of the schlafen core domain, preliminary biochemical studies of full length SLFN5 revealed increased nucleic acid binding properties towards DNA compared to SLFN51-336, as well as ATP-binding. These results imply that the predicted C-terminal helicase domain significantly contributes to DNA binding and is responsible for ATP turnover. Furthermore, 5.8 S rRNA was determined as potential substrate for full length SLFN5, since it was co-purified with SLFN5 from insect cells. Collectively, these results not only provide structural insights into the highly conserved slfn core domain, but also propose a new function on molecular basis for the schlafen protein family

The schlafen core domain: from structure to function

The immune system is a complex network of processes and structures to protect the organism against infectious diseases. All processes, which include the maturation of individual immune cells, must be strictly regulated to prevent malfunction. The schlafen protein family was recently reported to play key regulatory roles in T cell maturation and different subsets of individual schlafen family members are gradually upregulated during T cell maturation. The schlafen family belongs to the interferon-stimulated genes and various members play important roles in a plethora of cellular processes: regulation of the cell cycle, T cell quiescence, differentiation and proliferation of various cell types, tumorigenesis and inhibition of viral replication. All schlafen protein family members share the schlafen core domain, which is a highly conserved N- terminal region of approximately 340 amino acids. Based on sequence similarities, this region has been predicted to contain a divergent ATPase domain. Additionally, the longer schlafen protein members harbor a C-terminal domain with sequence homologies to superfamily 1 DNA/RNA helicases. Although the individual schlafen members play key roles in diverse cellular processes, they are poorly characterized in vitro and the underlying molecular mechanisms remain unknown. Since neither biochemical nor structural information were available, the overall goal of this study was to biochemically and structurally describe the schlafen proteins, and specifically their highly conserved schlafen core domain. Crystallographic studies performed during this thesis, revealed the structures of full length murine Schlafen 2 (Slfn2) and N-terminal human Schlafen 5 (SLFN51-336), which is the first high resolution structure of a human schlafen protein ever reported. Both crystal structures show a unique horseshoe shape with a novel fold harboring a highly conserved zinc finger. Interestingly, the schlafen core domain resembles no ATPase like fold and indeed, neither ATP-binding nor hydrolysis could be verified experimentally. Thus, structural information combined with experimental data prove that the schlafen core is no ATPase domain. Biochemical characterization discovered nucleic acid binding properties of the schlafen core domain. Binding affinities of SLFN51-336 increased in a length dependent manner for both, single-stranded DNA and RNA, although no preference for DNA or RNA could be identified. The highest affinity towards RNA was detected for a stem-loop structure and no binding for a RNA duplex, indicating that single-stranded regions are necessary for the interaction. The highest affinity of SLFN51-336 was measured with double-stranded DNA and the residues identified to be responsible for DNA binding were mapped to the zinc finger region by generating DNA-binding deficient mutants. Slfn2 was capable to bind both, DNA and RNA, with a 10 times higher affinity for both substrates than SLFN51-336. The 5S rRNA was identified by co-purification with Slfn2 as a potential nucleic acid substrate. Further biochemical investigations discovered a new function for SLFN51-336 and Slfn2, which is a 3’- 5’ exonuclease activity on single-stranded DNA in a metal ion-dependent, but ATP-independent manner. The importance of three conserved sites for DNA hydrolysis was confirmed by generating exonuclease-inactive mutants. However, the cleavage mechanism is not entirely solved and therefore a co-crystal structure of a substrate bound schlafen core domain would be of great benefit. Besides investigations of the schlafen core domain, preliminary biochemical studies of full length SLFN5 revealed increased nucleic acid binding properties towards DNA compared to SLFN51-336, as well as ATP-binding. These results imply that the predicted C-terminal helicase domain significantly contributes to DNA binding and is responsible for ATP turnover. Furthermore, 5.8 S rRNA was determined as potential substrate for full length SLFN5, since it was co-purified with SLFN5 from insect cells. Collectively, these results not only provide structural insights into the highly conserved slfn core domain, but also propose a new function on molecular basis for the schlafen protein family

Local and Global Explanations of Agent Behavior: Integrating Strategy Summaries with Saliency Maps

With advances in reinforcement learning (RL), agents are now being developed in high-stakes application domains such as healthcare and transportation. Explaining the behavior of these agents is challenging, as the environments in which they act have large state spaces, and their decision-making can be affected by delayed rewards, making it difficult to analyze their behavior. To address this problem, several approaches have been developed. Some approaches attempt to convey the $\textit{global}$ behavior of the agent, describing the actions it takes in different states. Other approaches devised $\textit{local}$ explanations which provide information regarding the agent's decision-making in a particular state. In this paper, we combine global and local explanation methods, and evaluate their joint and separate contributions, providing (to the best of our knowledge) the first user study of combined local and global explanations for RL agents. Specifically, we augment strategy summaries that extract important trajectories of states from simulations of the agent with saliency maps which show what information the agent attends to. Our results show that the choice of what states to include in the summary (global information) strongly affects people's understanding of agents: participants shown summaries that included important states significantly outperformed participants who were presented with agent behavior in a randomly set of chosen world-states. We find mixed results with respect to augmenting demonstrations with saliency maps (local information), as the addition of saliency maps did not significantly improve performance in most cases. However, we do find some evidence that saliency maps can help users better understand what information the agent relies on in its decision making, suggesting avenues for future work that can further improve explanations of RL agents

Human circulating T follicular helper cells during viral infection and autoimmunity

CD4+ T helper cells orchestrate the adaptive immune response. The differentiation of naïve CD4+ T cells into various functionally different subsets of T helper cells ensures the adaptation of the immune response to the invading pathogen. The T helper cell subset that is responsible for B cell help during affinity maturation in the germinal center (GC) reaction is called T follicular helper (Tfh) cells. Therefore, Tfh cells are crucial to develop long-lasting immunity by ensuring the generation of memory B cells and high-affinity antibody-producing plasma cells. Blood-resident Tfh cells, so called circulating Tfh (cTfh) cells, can be used to investigate human Tfh cells instead of lymphoid tissue-resident Tfh cells, which are difficult to assess in humans. Lymphoid tissue-resident Tfh cells and cTfh cells both provide B cell help and share similarities in phenotype and gene expression. cTfh cells can express other CD4+ T cell subset-defining chemokine receptors and can thereby be clustered into different subsets. Although increased cTfh cell frequencies have been connected to better vaccination outcome and new insights into cTfh cell kinetics might improve the understanding of established vaccinations and impact future vaccine design, only few studies investigated cTfh kinetics after vaccination. Most conclusions were drawn from annual influenza vaccinations that allow for investigation of recall responses. Nevertheless, it is difficult to distinguish between the primary and secondary immune response as vaccinees have likely been in contact with influenza virus before vaccination and additionally influenza vaccination can have low efficacy. Therefore, I tracked and characterized cTfh and other blood-resident immune cells by flow cytometry after challenge with a live virus in the context of a vaccination against yellow fever. Yellow fever virus (YFV) is endemic in tropical regions. Yellow fever vaccination elicits a strong, long-lasting immune response with neutralizing antibodies in almost all vaccinees. We were able to show that vaccination with the attenuated yellow fever virus elicited an increased frequency of activated cTfh cells from three days on after vaccination. The peak frequency of activated cTfh cells was detectable 14 days after vaccination. In addition, we observed a shift in the subset composition of cTfh cells during the immune response with cTfh1 cells as the most prevalent subpopulation. Those findings were confirmed by the detection of YFV-specific CD4+ T cells in the blood with major histocompatibility complex (MHC) II tetramers for four known epitopes. Moreover, we found a correlation of frequencies of cTfh1 cells with the strength of the neutralizing antibody response, which might influence future vaccine design. Tfh cells have also been implicated in the pathogenesis of several autoimmune diseases and are for example contained in ectopic lymphoid structures and implicated in the formation of autoantibodies. Multiple sclerosis (MS) often involves ectopic lymphoid structures and oligoclonal bands in the cerebrospinal fluid and multiple studies point to a role of Tfh cells in multiple sclerosis. Yet, cTfh cells and the impact of immunomodulatory drugs are not well investigated in patients with MS. Therefore, I compared blood-resident T and B cell populations of patients with multiple sclerosis, that either received no treatment or different immunomodulatory drugs, with cells derived from healthy donors. Although cTfh cells from MS patients were phenotypically not distinguishable from healthy donors, immunomodulatory treatment with the sphingosine-1-phosphate receptor (S1PR) 1 blocking drug fingolimod resulted in profoundly reduced frequencies of cTfh cells. Additionally, other T cells expressing the Tfh cell hallmark chemokine receptor CXCR5, such as T follicular regulatory cells and CXCR5+CD8+ T cells, were similarly affected. This provides insight into the migratory pattern of cTfh cells as well as a better understanding of the impact of fingolimod on blood-resident lymphocyte populations. In summary, the findings I present in this thesis contribute to a better understanding of circulating Tfh cells after viral challenge and immunomodulation. This might have implications for vaccine design and for the treatment of autoimmune diseases

Herdengesundheits- und Wohlbefindensplanung auf österreichischen Bio-Milchviehbetrieben

Herdengesundheits- und Wohlbefindenspläne stellen ein vielversprechendes Instrument zur kontinuierlichen Verbesserung von Tiergesundheit und Wohlergehen auf tierhaltenden Betrieben dar. Dieses Konzept wurde im Rahmen des europäischen ERANet-Projektes CORE Organic ANIPLAN auf 39 österreichischen Bio-Milchviehbetrieben angewendet. Ziel der Studie war es (1) die Herdengesundheits- und Wohlbefindenssituation auf den Betrieben zu erfassen, (2) Herdengesundheits- und Wohlbefindenspläne auf den Betrieben einzuführen und (3) eine Evaluierung der Herdengesundheits- und Wohlbefindenssituation bzw. eine Effektivitätskontrolle der umgesetzten Maßnahmen nach dem Planungsprozess durchzuführen. Die Erfassung der Herdengesundheits- und Wohlbefindenssituation am Betrieb erfolgte gemäß einer leicht angepassten Version des Welfare Quality® Erhebungsprotokolls für Milchkühe. Der Prozess der Herdengesundheitsplanung folgte den sieben Prinzipien, die im Rahmen des Projektes CORE Organic ANIPLAN definiert wurden. Erste Ergebnisse ausgewählter Parameter zeigen über alle Projektbetriebe hinweg unabhängig vom Interventionsbereich und Umsetzungsgrad der Interventionsmaßnahmen keine signifikante Veränderung zwischen den Projektjahren 2008 und 2009. Auf Betrieben, die aktiv Interventionsmaßnahmen umsetzten, konnte eine signifikante Reduktion der Hautschäden und –veränderungen beobachtet werden. Die Lahmheitsprävalenz sowie die durchschnittliche Zellzahl blieben hingegen auch auf den Interventionsbetrieben unverändert

Benchmarking Perturbation-based Saliency Maps for Explaining Deep Reinforcement Learning Agents

Recent years saw a plethora of work on explaining complex intelligent agents. One example is the development of several algorithms that generate saliency maps which show how much each pixel attributed to the agents' decision. However, most evaluations of such saliency maps focus on image classification tasks. As far as we know, there is no work which thoroughly compares different saliency maps for Deep Reinforcement Learning agents. This paper compares four perturbation-based approaches to create saliency maps for Deep Reinforcement Learning agents trained on four different Atari 2600 games. All four approaches work by perturbing parts of the input and measuring how much this affects the agent's output. The approaches are compared using three computational metrics: dependence on the learned parameters of the agent (sanity checks), faithfulness to the agent's reasoning (input degradation), and run-time.Comment: Presented on the Explainable Agency in Artificial Intelligence Workshop during the 35th AAAI Conference on Artificial Intelligenc

Establishing Native Grasses in a Big Sagebrush–Dominated Site: An Intermediate Restoration Step

Many semiarid rangelands in the Great Basin, U.S.A., are shifting dominance to woody species as a consequence of land degradation including intense livestock grazing and fire suppression. Whereas past rehabilitation efforts in Big sagebrush (Artemisia tridentata) steppes removed the shrub and added introduced forage grasses to successfully shift communities from shrublands to grasslands, current consensus is that native species should be included in restoration projects and that retention of some woody plants is desirable. We examined the potential for interseeding grasses into dense shrub communities as a precursor to thinning shrubs and releasing grasses from shrub interference. We compared seedling establishment of the native grass, Bluebunch wheatgrass (Pseudoroegneria spicata), with that of the Eurasia grass, Crested wheatgrass (Agropyron desertorum), in dense Ar. tridentata stands. Shrubs may play an important role as nurse plants for seedling establishment (reduced solar radiation, ‘‘island of fertility’’ effect) but result in highly contrasting light environments and root interference for seedlings. In experimental plots, we examined effects of Ar. tridentata shade levels (0, 40, 70, and 90% reduction of solar radiation) and initial root exclusion (present/absent) on the establishment and growth of P. spicata and Ag. desertorum seedlings. With this design we evaluated the interference effects of Ar. tridentata on the two grasses and identified the most beneficial microsites for grass restoration in Ar. tridentata– dominated communities. We predicted seedling survival and growth to be greater under moderate shade (40% reduction) and limited root competition than under no or strong shade conditions (0 and 90%) and unrestricted root interactions. Fifty to 85% of the P. spicata and Ag. desertorum seedlings survived the dry summer months of 1995 and 1996 and the intervening winter. Neither shading nor root exclusion from Ar. tridentata affected final seedling survival of either species. Seedling biomass of both grass species was negatively affected by initial root interactions with Ar. tridentata. However, the analysis of seedling biomass variability (coefficient of variation) indicated that in all shade and root-exclusion treatments, some seedlings of both species developed to large individuals to survive in Ar. tridentata–dominated rangelands. Thus, the use of interseeding techniques shows promise for restoring herbaceous species in dense Ar. tridentata stands and should be given further consideration when shrub retention is an important consideration