Hematopoietic stem cell transplantation (HSCT) is used to treat patient with hematological diseases such as leukemia and genetic conditions such as sickle cell anemia. After HSCT the patients are supervised for signs of relapse of disease or rejection of transplanted cells. This is done by using chimerism analysis. At the department of clinical genetics at Akademiska sjukhuset fragment analysis of short tandem repeats is used for chimerism analysis, which is to be replaced by a Next generation sequencing (NGS) based method called Devyser chimerism, which includes an IVDR labelled kit. The aim of this project was to validate the new method for chimerism analysis. DNA samples from twelve HSCT patients and their donors were analyzed with Devyser chimerism and the results were compared to the results from the current method. The sensitivity of the new method was tested by analysis of artificial chimerism samples from blood donors. The results from the comparison showed a good correlation between methods (R2 = 0,9864) and the sensitivity of the method was confirmed to be 0,1% mixed chimerism. There was some difficulty in identifying enough informative markers for re-transplanted patients two had separate donors. This is a known problem for chimerism analysis in general and not a specific problem to the new method and will not be a hindrance for the implementation of Devyser chimerism at the clinical laboratory.

Better methods and tools are needed in the fight against child pornography. This thesis presents a method for file type categorisation of unknown data fragments, a method for reassembly of JPEG fragments, and the requirements put on an artificial JPEG header for viewing reassembled images. To enable empirical evaluation of the methods a number of tools based on the methods have been implemented. The file type categorisation method identifies JPEG fragments with a detection rate of 100% and a false positives rate of 0.1%. The method uses three algorithms, Byte Frequency Distribution (BFD), Rate of Change (RoC), and 2-grams. The algorithms are designed for different situations, depending on the requirements at hand. The reconnection method correctly reconnects 97% of a Restart (RST) marker enabled JPEG image, fragmented into 4 KiB large pieces. When dealing with fragments from several images at once, the method is able to correctly connect 70% of the fragments at the first iteration. Two parameters in a JPEG header are crucial to the quality of the image; the size of the image and the sampling factor (actually factors) of the image. The size can be found using brute force and the sampling factors only take on three different values. Hence it is possible to use an artificial JPEG header to view full of parts of an image. The only requirement is that the fragments contain RST markers. The results of the evaluations of the methods show that it is possible to find, reassemble, and view JPEG image fragments with high certainty.

Accurate energetic modeling of large molecular systems is always desired by chemists. For example, ligand-protein binding simulations and enzymatic catalysis studies all involve with a small energy difference. The energetic accuracy depends largely on a proper handling of electronic correlations. Molecular mechanics (MM) methods deliver a parameterized Newtonian treatment to these problems. They show great capability in handling large calculations but give only qualitatively good results. Quantum mechanics (QM) methods solve Schrödinger equations and exhibit much better energy accuracy, though the computational cost can be prohibitive if directly applied to very large systems. Fragment-based methods have been developed to decompose large QM calculations into fragment calculations. However, most current schemes use a self- consistent field (SCF) method on fragments, in which no electronic correlation is accounted for. The super-system energy is computed as a sum of fragment energies plus two-body corrections and, possibly, three-body corrections (a "body" is a fragment). Higher order corrections can be added. Nevertheless, many problems require the treatment of high order electronic correlations. The coupled-cluster (CC) theory is the state-of-the-art QM method for handling electronic correlations. The CC wavefunction contains correlated excitations up to a given truncated level and coincidental excitations for all possible electronic excitations. It is a brilliant way of including more electronic correlations while maintaining a low-order scaling. In the proposed excitonic coupled-cluster (X-CC) theory, substantial modifications have been made to allow CC algorithms to act on the collective coordinates of fragment fluctuations to obtain super-system energy. The X-CC theory is designed to achieve accurate energetic modeling results for large chemical systems with much improved affordability and systematic improvability. The test system used in this work is a chain of beryllium atoms. A 30-fragment X-CCSD(2) calculation delivered matching accuracy with traditional CCSD method. An X-CCSD(2) calculation on a chain of 100 bonded fragments finished in 7 hours on a single 2.2 GHz CPU core. The X-CC scheme also demonstrates the ability in handling charge transfer problems. Due to the use of fluctuation basis in the test cases, the excitonic algorithms can be easily generalized to inhomogeneous systems. This will be investigated in future work.

This paper presents how I came to create this collection of jewellery that is intimately tied to memories and fragments. How I have conducted my research about collections, museums, jewellery, and artists. Incorporating those findings into the workshop and the way the pieces came to be. Made in silver, zinc and iron, and with use of the techniques casting and etching.  And conclusively how a collection took form with this idea to give a sense of treasures or a language from an unknown world or place. Somewhere where time has passed and the individual pieces convey the notion that they are fragments of a greater whole, part of a story or memory that we can sense but not quite reckon, not to be fully understood.

I denna uppsats används fragmentsestetik som metod för att analysera berättartekniken i Jacob’s Room av Virginia Woolf. Receptionskritik av romanen och teoribildningen kring fragmentsestetik inleder. Därefter undersöks hur teorin påverkar läsningen. Vidare förklaras hur olika teman kan hålla samman den ofta uppbrutna intrigen. Därtill tydliggörs hur fragmentsestetiken påverkar gestaltningen av huvudpersonen Jacob. Huvudpersonen sätts också in i ett modernistiskt sammanhang och hans gestalt analyseras i relation till staden. Modernismens begrepp flanör undersöks och huruvida Jacob kategoriseras som sådan. Avslutningsvis diskuteras den moderna stadens gestaltning och funktion. Fragmentsestetiken sätter texten i rörelse då London och dess invånare omväxlingsvis speglas som objekt och subjekt. Således bildas enhetlighet och brottstycken av den intrig som utgör romanen. / <p>Slutgiltigt godkännandedatum: 2023-08-24</p>

Huntington disease (HD) is a devastating and fatal neurodegenerative disease. At the moment, no disease modifying therapies are available, with only symptomatic treatment offered to alleviate psychiatric and some types of motor deficits. As a result, many people will continue to suffer and die from this disease. Small molecule therapies have failed to provide benefit in HD, necessitating more complex gene therapy approaches and the identification of less traditional therapeutic targets. A previous study demonstrated that preventing cleavage of the huntingtin (HTT) protein, the protein that when mutated causes HD, by caspase 6 (C6) at amino acid 586 prevents the onset of disease in transgenic HD model mice. This suggests that inhibiting the toxicity initiated by N586 cleavage could be a promising therapeutic strategy, but a safe and specific way to do this in humans has not been identified. General C6 inhibition is not a feasible strategy due to the vital functions it plays throughout life. Thus, the purpose of this study was to investigate whether the C6 cleavage fragment of HTT, N586, is itself a toxic species of HTT or if it initiates a toxic proteolytic pathway in order to identify more viable therapeutic strategies for HD. To accomplish this, we are using novel and highly sensitive immunoprecipitation and flow cytometry (IP-FCM) protein detection assays, specific for the N586 neoepitope of HTT, to evaluate the in vivo persistence of N586 in HD model mice. If N586 is detected, it is likely that it is itself toxic and promoting its degradation may be beneficial. Conversely, if it is not detected, N586 cleavage likely initiates a toxic degradation pathway and promoting its stability may be beneficial. The results of these studies have the potential to define new therapeutic strategies for HD that can be addressed more specifically than generalized C6 inhibition for the prevention of N586-mediated toxicity. The selective targeting of N586 toxicity, either to promote or prevent its degradation depending on our results, would ensure that therapeutic activity is restricted to HTT and reduce the potential for deleterious off-target effects

<p>MurA catalyzes the first committed step of peptidoglycan biosynthesis and it is the target of the antibiotic fosfomycin. Due to a Cys-to-Asp substitution in the active site, MurAs from a number of pathogenic bacteria, including <em>Mycobacterium tuberculosis</em> and <em>Borrelia burgdorferi</em> (Lyme disease), are fosfomycin resistant. His-tagged <em>Borrelia burgdorferi</em> MurA (Bb_MurA) and its D116C mutant have been successfully expressed, purified and characterized. The <em>k</em>_cat value of wild-type Bb_MurA was 0.74 ± 0.01 s^-1. The D116C mutant’s <em>k</em>_cat decreased by 25-fold and was fosfomycin sensitive. The pH profiles of <em>k</em>_cat for both Bb_MurA and its mutant were characterized. There was little difference in p<em>K</em>_a1 values, but the p<em>K</em>_a2 value shifted from 7.4 ± 0.2 in wild-type enzyme to a value >11 in the mutant. This demonstrated that the p<em>K</em>_a2 of 7.4 was due to D116, and that it must be protonated for activity. Fosfomycin inactivation of Bb_MurA_H6(D116C) was time-dependent and only proceeded in the presence of UDP-GlcNAc. The dissociation constant, <em>K</em>_i, was 5.7 ± 0.4 µM and rate of covalent modification, <em>k</em>_inact, was 0.021 ± 0.003 s^-1.</p> <p>DAHP synthase catalyzes the first committed step in the shikimate pathway, and its catalysis has been proposed to proceed through two oxacarbenium ion intermediates. Pyruvate oxime, glyoxylate oxime and 4-imidazolecarboxylic acid have been evaluated as inhibitors of DAHP synthase. In the presence of glycerol 3-phosphate, the fitted <em>K</em>_i values of pyruvate oxime and glyoxylate oxime were 7.6 (± 0.9) × 10^-5 M and 7.4 (± 1.7) × 10^-5 M, respectively. 4-Imidazolecarboxylic acid’s inhibition was cooperative, and its binding was competitive with respect to PEP, and uncompetitive with respect to E4P. Its equilibrium dissociation constant was 3.0 (± 0.2) × 10^-3 M.</p> / Master of Science (MSc)

<p dir="ltr">Humans encode approximately 100 deubiquitinating enzymes (DUBs) which are categorized into seven distinct subfamilies. Each family and representative has a unique expression, function and binding topology to ubiquitin. In addition to human DUBs, parasites, bacteria, and viruses contain DUBs with unique structures and functions. One subfamily of DUBs, the ubiquitin C-terminal hydrolases (UCH), has four structurally similar human members and two known members within the <i>Plasmodium falciparum</i> genome. Human UCHL1 and UCHL3 are genetically validated targets in oncology and <i>Plasmodium falciparum</i><i> </i>UCHL3 (PfUCHL3) is a prospective target for antimalarial drug development. Though these three UCH enzymes have potential as therapeutic targets, there is a significant lack of quality small molecule chemical probes to understand the underlying biology and function of the enzymes, pharmacologically validate the targets, and serve as leads for drug development in oncology and malaria.</p><p dir="ltr">The UCH enzymes are cysteine proteases, which our lab has leveraged to identify novel covalent small molecule inhibitors of each enzyme. The workflow for each hit identification and optimization campaign is similar. Covalent fragment screening of electrophilic small molecule libraries against the respective recombinant enzyme was performed to identify chemical space around each enzyme. Subsequent medicinal chemistry hit-to-lead optimization was undertaken to improve upon the moderately potent hit molecules to provide improved small molecule inhibitors for each enzyme. Inhibitor identification and optimization for UCHL1 is described in Chapter 2, revealing a novel scaffold and a cocrystal structure reveals a unique binding pose for UCHL1 inhibitors. These molecules were also characterized in breast cancer cells to validate UCHL1 as a therapeutic target in breast cancer. First-in-class covalent inhibitors of UCHL3 are described in Chapter 3. Medicinal chemistry optimization along with a cocrystal structure of the initial hit has revealed the molecular interactions of this novel inhibitory scaffold. PfUCHL3 inhibitor identification is described in Chapter 4. Characterization of these molecules against Plasmodium falciparum is described along with a comparison to a recently identified reversible PfUCHL3 inhibitor. Finally, conclusions and future directions toward the development of potent, drug-like inhibitors of each UCH enzyme is presented in Chapter 5.</p>

L'étude de la représentation de la maladie d'Alzheimer dans Le monde de Barney de Mordecai Richler, de Trois-Pistoles et les Basques, le pays de mon père de Victor-Lévy Beaulieu et de "Je ne suis pas sortie de ma nuit", d'Annie Ernaux permet d'esquisser les contours d'une spécificité littéraire de la maladie, bien au-delà du thème de l'oubli. N'envisager la maladie d'Alzheimer qu'en termes de dégénérescence cognitive, c'est évacuer sa dimension de matériau littéraire qui influence tant la construction que le style d'un texte. L'analyse de trois récits contemporains permet l'identification de procédés rhétoriques mais aussi de stratégies narratives et stylistiques qui servent à circonscrire l'empreinte littéraire propre à la maladie d'Alzheimer. La prise en charge du récit par un tiers parti explique la thématique de la filiation qui donne à voir la maladie de l'intérieur et de l'extérieur. L'oeuvre de création s'inscrit dans ce travail d'archivage de la mémoire familiale. Une petite-fille s'adresse indirectement à sa grand-mère qui souffre de la maladie d'Alzheimer. Nous suivons l'évolution de la maladie et sommes témoins de l'effritement des souvenirs et du discours de la grand-mère. / The study of the Alzheimer's disease representation in Mordecai Richler's Barney's Version, Victor-Lévy Beaulieu's Trois-Pistoles et les Basques, le pays de mon père and Annie Ernaux's "Je ne suis pas sortie de ma nuit" allows us to outline the disease's literary specifics, beyond the theme of cognitive degeneration is to evacuate its dimension as a literature material which influences the structure of a text as well as its style. The analysis of three contemporary stories contributes to the identification of rhetorical methods as well as narrative and style strategies which help us to delimit the Alzheimer's disease literary mark. We will see that when a third party takes charge of the story, it explains the filiation theme which helps to see the disease from the inside as well as from the outside. It also shows an archiving work. The creation part of the essay fits into the archiving process of the family's memory. A grand-daughter talks indirectly to her grand-mother who suffers from Alzheimer's disease. We follow the evolution of the disease and we witness the erosion of the grand-mother's memories and speech.

Les textes de l’écrivain argentin Juan José Saer (1937-2005) construisent une œuvre unique à partir d’un processus typiquement balzacien, la récurrence des personnages dans un lieu, la « zona », donnant l’impression de créer une « comédie humaine » ou une saga. Mais la fragmentation, qui traverse l’ensemble du corpus tant dans la récurrence (de personnages, lieux, situations, temps), que dans l’intrigue, la représentation du réel ou l’écriture, introduisant de l’hétérogénéité et de l’indétermination, le rapprocherait plutôt du Nouveau Roman. C’est donc la fragmentation, plutôt qu’une unité préétablie, qui donne sa cohérence à l’ensemble. La « théorie négative » de Saer, qui lui permet d’écrire contre certains modèles perçus comme « totalitaires », s’articule de façon cohérente avec la place importante qu’il laisse au lecteur, dans les interstices entre deux fragments. La cohérence de l’ensemble est un effet de lecture délibéré et, plus que l’auteur, c’est désormais le lecteur qui est le garant de l’unité de l’œuvre. / Together, the texts written by Argentinian author Juan José Saer (1937-2005) build a unique opus, through the typically Balzacian process of recurring characters staged within a setting, « la zona », in a saga bearing some resemblance to Balzac’s « comédie humaine». But the fragmentation that pervades the body of work, not merely in its recurring motifs or structures (characters, settings, situations, time-frames), but in its very plot, its representation of reality and its aesthetics of the heterogenous and the indeterminate, rather liken it to the « Nouveau Roman ». Fragmentation, rather than a pre-established unity, gives the work its coherence as a whole. Saer’s « negative theory », which allows him to write against a number of models he perceives as « totalitarian », is coherently articulated with the essential role given to the reader, in the gaps between two fragments. The coherence of the whole relies on reader reception ; rather than with the author, the unity of the opus rests with the reader her/himself.