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  • Disputas: 2024-08-22 13:00 Cramérrummet (mötesrum 12), hus 1, Albano, Stockholm
    Farahbakhsh Touli, Elena
    Stockholms universitet, Naturvetenskapliga fakulteten, Matematiska institutionen.
    Graphical Models: Mathematical Foundation and Statistical Analysis2024Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Working on different problems related to graph theory combined with statistics is the main purpose of this thesis. 

    In paper I, we worked on the distance between trees and defined another definition for the interleaving distance that was already introduced for determining the distance between merge trees. The new definition was based on only one map from one of the trees to another one. Therefore, we could gain fixed-parameter tractable algorithms for finding the interleaving distance between merge trees with some conditions. 

    In paper II, we worked on the clustering coefficient of the networks. The clustering coefficient indicates the tendency of the vertices of the network to form a triangle. We introduced another clustering coefficient, which we called it Relative clustering coefficient. Finally, the importance of the relative clustering coefficient. 

    In paper III, we worked on the financial relationship between companies in Sweden, and we used two methods (the Pearson correlation coefficient (PCC) and the generalized variance decomposition (GVD). We then ap- plied these methods to the financial data consisting of the daily returns on the 28 stocks included in the computation of the OMX index (the index of the Swedish capital market). 

    Gaussian Graphical Model is the main subject of paper IV. In this paper, we consider three types of precision matrices, and corresponding to each type of precision matrix, we develop the exact test theory. Finally, the new approaches are compared to the benchmark method via an extensive simulation study. 

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    Graphical Models: Mathematical Foundation and Statistical Analysis
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  • Disputas: 2024-08-23 09:00 Air & Fire (Gamma 2), SciLifeLab, Solna
    Sekar, Vaishnovi
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för molekylär biovetenskap, Wenner-Grens institut.
    MicroRNA biogenesis and function in single cells2024Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    microRNA are short non-coding RNAs and important post transcriptional gene regulators. miRNAs are found in all animals that have been studied, in numbers that largely correlate with organismal complexity. For instance, nematodes have around 200 miRNA genes, while humans have more than 600 miRNA genes. Mutant animals that are deficient in miRNAs generally exhibit gross developmental defects or embryonic lethality, underlining the importance of these regulators. Given that an estimated ~60% of human mRNAs are targeted by miRNAs in some cellular context, it is not surprising that these regulators are involved in numerous biological processes, ranging from the formation of cell identity to development and human diseases. Even though miRNAs have been systematically studied for over a decade, fundamental questions regarding their biogenesis and function remain unanswered. microRNAs are unevenly distributed between cell types and within homogeneous cell populations, affecting the transcriptomes of individual cells. The vast majority of miRNA studies have been conducted on large pools of cells, and little is known about the biogenesis and function in individual cells. To understand their effect on gene regulation, single-cell measurements are crucial. This thesis introduces techniques that allow us to extend our understanding about microRNA at the resolution of single cells.

    In Paper I, we develop and establish agoTRIBE – the first sequencing-based method to measure regulatory interactions between miRNAs and their mRNA targets transcriptome-wide in single cells. We applied Smart-seq3 single-cell RNA sequencing to detect increased editing transcriptome-wide in key miRNA targets and found substantial differential targeting across the cell cycle and in mixed cell populations. This method overcame limitations of current methods and allowed for study of heterogeneity in miRNA targeting across individual cells. In Paper II, we further explored miRNA targeting landscape in single cells using agoTRIBE and revealed differential targeting within homogenous cell populations. We observe two groups of cells with overlapping but distinct targeting patterns and provide evidence that miRNAs act on different groups of genes with distinct biological functions. In paper III, we proposed a method 'micro-imp' to infer miRNA activity from existing single cell RNA-sequencing (scRNA-seq) data, to overcome the limitation of low sensitivity in direct miRNA sequence of single cells. We show significant positive correlation between the inferred activity and the measured miRNA expression suggesting that this approach can be utilised to obtain orthogonal information from existing scRNA-seq datasets. In paper IV, we provide valuable insights from miRNA profiling in single cells and together with integration of scRNA-seq data from the same study system. We highlight heterogeneity in miRNA expression across single cells and link it to the variation and covariation of the target pool. Further, we detect large parts of pri-miRNA transcripts in single cells devoid of biogenesis factors, an aspect previously underexplored. The work presented in this thesis focus on methods and techniques to expand our understanding of miRNA biology at single cell resolution. 

     

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    MicroRNA biogenesis and function in single cells
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  • Disputas: 2024-08-23 13:00 sal FB42, AlbaNova universitetscentrum, Stockholm
    Hörnquist, Johan
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    A unified model of reactive scattering processes: Application to the H2 reaction complex2024Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    In this thesis, reactive scattering processes involving the H2 reaction complex are studied ab initio and fully quantum mechanically. These processes have in common that they involve highly excited electronic states, which could be either bound or resonant. Non-adiabatic couplings, which can be significant both at small and large internuclear distances, need to be included to account for the interaction between the bound electronic states. In addition, the electronic resonant states interact with the ionization continuum at small internuclear distances, which may cause the collision complex to autoionize. In this work, a model is developed which incorporates these different coupling mechanisms. By introducing a quasidiabatic model at small internuclear distances, resonant states and couplings to the ionization continuum are incorporated. The quasidiabatic model is combined with a strict diabatic description, which rigorously incorporates non-adiabatic couplings among the bound electronic states. Nuclear dynamics are solved for using a close-coupling approach in a strict diabatic representation, where a non-local complex potential is included to account for loss into the ionization continuum. With this model, various reactive scattering processes can systematically be studied using the same set of potential energy curves and couplings. The model is applied in studies of H++H- mutual neutralization, H(1s)+H(ns) and H++H- associative ionization as well as dissociative recombination and resonant ion-pair formation in electron collisions with HD+. Cross sections and branching ratios are compared with results from previous experiments and theoretical studies.

    Fulltekst (pdf)
    A unified model of reactive scattering processes: Application to the H2 reaction complex
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  • Disputas: 2024-08-23 13:00 hörsal 9, hus D, Stockholm
    Savola, Kristiina
    Stockholms universitet, Humanistiska fakulteten, Institutionen för slaviska och baltiska språk, finska, nederländska och tyska.
    Rajanvetoja ja vastakkainasetteluja: Diskursiiviset strategiat suomalaisten poliitikkojen blogiteksteissä vaalivuonna 20152024Doktoravhandling, monografi (Annet vitenskapelig)
    Abstract [en]

    In this monograph thesis, I examine political confrontations, their actors, conflict lines, discursive strategies, linguistic means, and related topics in Finnish politicians’ blog texts. Additionally, I analyse the occurrences of populist communication styles within these politicians’ blog discourses.

    The data consists of blog texts from nine ideologically diverse politicians from the Finnish parliamentary election year of 2015. The study is grounded in Critical Discourse Studies (Reisigl & Wodak 2016) and employs methods of rhetorical-performative discourse analysis (Palonen & Saresma 2017), along with political theories of politics and populism (Laclau 2005; Moffitt 2016; Mouffe 2005, 2013; Palonen 2020).

    The first part of the analysis explores the core topics in the data: economic politics and immigration politics, along with their related discourses. Discourses on economic politics in the blogs of government politicians include defending the welfare state, and advocating for citizens’ equalisation, viewing citizens as a socio-economically homogeneous group. Additionally, they address confrontation as a political obstacle and the necessity of economic measures. Opposition politicians' blogs, on the other hand, feature a discourse defending citizens against the government’s planned and implemented economic cuts.

    Discourses on immigration politics in government politicians’ blogs frame asylum seekers as a threat and migration as a cause of societal polarisation in Finland, while also opening up a human right discourse that views asylum seekers from a humanitarian perspective. In opposition politicians’ blogs, the predominant discourse defends asylum seekers.

    These topics are linked to ongoing global crises, such as the so-called refugee crisis and the aftermath of the 2008 economic crisis. Government politicians focus on their impacts on Finland and Europe, while opposition politicians emphasise Finland’s role as a responsible actor and mediator in international politics.

    The second part of the analysis examines conflict lines, discursive strategies, and linguistic means involved in confrontations. Strategic dimensions of the confrontations include a populist division between ‘the people’ and ‘the elites’, as well as between ‘the people’ and media and researchers. Strategies also involve affective defence of socially vulnerable groups, ideological opposition, equalisation of citizens, consensus-seeking, holding citizens accountable, and community building.

    Confrontations occur at the level of discursive strategies, lexical, metaphorical, rhetorical, and structural choices in the blog texts, and in the intertextual relations between the texts. Linguistically, these confrontations are produced through negative labelling of opponents, actor-distancing generic constructions (passive verbs, and the Finnish zero person), metaphors like water, war, sport, and the nation as a body, as well as empty and floating signifiers, euphemisms, antitheses, and irony.

    In summary, confrontation is a political positioning strategy used to legitimise politicians’ positions and agendas, create and maintain in-groups and out-groups, and defend them from hypothetically threatening actors and forces, who in turn are delegitimised. Additionally, confrontations are utilised to shape perceptions of political reality, criticise, and highlight other actors’ responsibilities.

    Fulltekst (pdf)
    Rajanvetoja ja vastakkainasetteluja
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  • Disputas: 2024-08-26 13:00 hörsal 7, hus D, våning 3, Stockholm
    af Edholm, Kristoffer
    Stockholms universitet, Humanistiska fakulteten, Institutionen för etnologi, religionshistoria och genusvetenskap.
    Ascetic poetry in ancient India: The ideal renouncer and the path to liberation, according to independent verses in early Brahmanic, Buddhist, and Jaina literature2024Doktoravhandling, monografi (Annet vitenskapelig)
    Abstract [en]

    The dissertation identifies the ideal renouncer and the path to liberation on the basis of nearly 3500 “independent verses”, i.e. one-strophe stanzas (gāthās, ślokas), in early Brahmanic, Buddhist, and Jaina literature, including Mahābhārata, Suttanipāta, Dhammapada, Saṃyuttanikāya, Uttarajjhayaṇa, Sūyagaḍa, Isibhāsiyāiṃ, and other texts. It is argued that this genre of poetry is important for our knowledge about the ascetic milieu in Northern India around the 5th century BCE.

    Verses from the three traditions are compared with one another, the verse-material is compared with selected texts belonging to other genres, and the literature is placed in its historical context. Attention is given to vocabulary, formulas, similes, and recurrent themes. Hypotheses about the early history of the renouncer-traditions are tested against the verse-material.

    Part 1 discusses aim, theory, method, terminology, previous studies, earliness and authenticity of the verses, origins and characteristics of the genre, and relevant texts. Part 2 treats the debated origins of emancipatory askesis, brāhmaṇa and śramaṇa, authority and founder-figures, and female ascetics. Part 3 proceeds along an ideal path to liberation: from reasons for giving up mundane pursuits, to going forth into homelessness, practise of austerity, itinerancy, solitude, seclusion, mendicancy, purification, non-harm, restraint, heroic overcoming of obstacles, and meditation, to attainment of gnosis and awakening, and finally liberation from saṃsāra. Part 4 is the conclusion. The Appendices contain the entire verse-material, as well as defining sentences in final pādas, shared whole verses, and key-terms.

    It is concluded that in the three verse-corpora one can identify a shared outlook, which is world-rejecting, autocentric, and telos-oriented, and a shared renouncer-ideal, which is male, heroic, and austere. The same outlook and ideal are found in narrative accounts about Śākyamuni, Mahāvīra, and others who attain the highest goal. Differences between the three traditions concern mainly the use of certain terms, formulas, and similes, less so doctrine, but the differences are not reducible to a divide between Brahmanic and Buddhist/Jaina.

    Generally speaking, each tradition has composed its own verses that promote a renouncer-ideal and a path to liberation, rather than having borrowed verses from another tradition or from a common source. The many similarities between the three traditions are primarily due to their common origin in the ascetic milieu, in which the one-strophe gāthā was an established literary medium for making authoritative statements.

    It is argued that the shared outlook and ideal were established before the introduction of two-step ordination, nuns’ order, fourfold community, devotion to an exalted founder-figure, and the building of monasteries. The verse-content points to a rural environment and a stratified society rooted in late Vedic culture. The renunciant movement of the 5th century BCE can be seen as the culmination of a centuries-old ascetic tradition in ancient India.

     

    Fulltekst (pdf)
    Ascetic poetry in ancient India: The ideal renouncer and the path to liberation, according to independent verses in early Brahmanic, Buddhist, and Jaina literature
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  • Disputas: 2024-08-30 13:00 Pärlan, hus 1, plan 6, Albano, Stockholm
    Schmidt-May, Alice Frederike
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    State-Resolved Mutual Neutralization Experiments on Atomic Hydrogen Anions: H- with Li+, O+, N+, and C+2024Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    This thesis presents experimental studies of mutual-neutralization reactions between H- and the cations 7Li+, 16O+, 12C+ and 14N+ at the double electrostatic ion-beam storage ring DESIREE. By overlapping two keV ion beams, with corresponding speeds of ca. 1000 km/s, and matching their velocities with applied electric fields, the center-of-mass collision energies are reduced to a few tens of meV. Time- and position-sensitive detectors allow the measurement of the  separation of the two formed neutral products, which depends on the kinetic-energy release in the charge-transfer reaction. The branching fractions into the different quantum states are extracted by binning or modelling of the measured product-separation distributions.

    Due to the difficulty of merged-beams experiments with high mass ratio between the ions, 1H- is often replaced with 2H-. We were able to merge beams with a mass ratio of up to 16 between the ions, which allowed us to use 1H- in all studies presented here. For H-+7Li+ and H-+16O+, we included both hydrogen isotopes, and found a significant isotope effect. The lighter hydrogen isotope leads to an increased population in lower excited states in both cases.

    Our data constitute important benchmarks for theoretical calculations that are needed in the modelling of stellar photospheres.We compare our experimental findings to different theoretical models and discuss their strengths and shortcomings.

    In order to achieve these scientific results, the thesis work involved the development of data preparation and analysis for a frame- and an event-based detector, as well as the development of experimental methods.

    Fulltekst (pdf)
    State-Resolved Mutual Neutralization Experiments on Atomic Hydrogen Anions: H- with Li+, O+, N+, and C+
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