Publikationer från Uppsala Universitet
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Displaced Muon Detection Using Machine Learning : ATLAS L0 Muon Trigger Upgrade
No full textThis work presents the development and evaluation of lightweight convolutional (CNN) and recurrent neural network (RNN) architectures for real-time muon triggering in the ATLAS Muon Spectrometer using Monitored Drift Tube (MDT) hit data. Addressing a critical need in modern particle physics, the models were specifically designed to efficiently detect not only prompt muons but also displaced muons, which are key signatures for new physics scenarios such as long-lived particles. The architectures were optimized to meet stringent hardware constraints, achieving high classification accuracy for both prompt and displaced muons, with true positive and truen egative rates exceeding 0.9 in some cases. Extensive training and validation on simulated data—including dark photon decays with varying parameters—as well as real background data, demonstrated robust generalisation and the ability to distinguish between different muon signatures. The neural networks were successfully converted to high-level synthesis (HLS) for FPGA implementation, with post-conversion validation confirming the viability of deployment despite anobserved reduction in accuracy. This study establishes a foundation for machine learning-based trigger systems in high-energy physics, highlighting the importance of displaced muon detection and the potential for further optimisation, integration with additional detector information, and expansion toward adaptive, physics-aware triggering strategies in future ATLAS upgrades. Detta projekt undersöker hur maskininlärning kan hjälpa forskare vid ATLAS experimentet, som är en del av Large Hadron Collider, att mer effektivt upptäcka speciella typer av partiklar som kallas myoner. Myoner är viktiga eftersom de kan ge ledtrådar om ny, ännu oupptäckt fysik – särskilt när de uppträder långt ifrån platsen där partikelkollisionen ägde rum, vilket kallas att de är ”förskjutna”. Genom att träna datorbaserade modeller att snabbt och noggrant identifiera både vanliga och förskjutna myoner i realtid, visade vi att maskininlärning pålitligt kan skilja riktiga myonsignaler från bakgrundsbrus. Dessa modeller har noggrant utformats för att fungera på den snabba, specialiserade elektronik som används i experimentet, och våra resultat visar att de kan anpassas för användning i den faktiska ATLAS-detektorn. Detta arbete är ett viktigt steg mot framtida partikelupptäckter genom att förbättra hur vi hittar dessa sällsynta och ovanliga myonhändelser
När innovation bankar på dörren öppnar man : En komparativ studie av innovationsarbetet på nisch- och storbanker
No full textBanksektorn står inför omfattande teknologiska förändringar där molnbaserade plattformar utmanar traditionella legacy-system. Denna studie undersöker hur storbanker och nischbanker skiljer sig åt i sitt innovationsarbete, med fokus på hur valet av bankplattform påverkar deras förmåga att identifiera, implementera och integrera ny teknologi. Genom en kvalitativ komparativ fallstudie av fem svenska banker och med stöd i Teece’s Dynamic Capabilities Framework, Resource-Based View (RBV) samt teorin om Path Dependency, visar studien att nischbanker, med modern molninfrastruktur och integrerade strukturer, uppvisar högre organisatorisk rörlighet och större förmåga att omsätta teknologiska möjligheter i praktisk innovation. Storbanker, däremot, bromsas av tekniska arv och organisatorisk struktur. Studien bidrar med fördjupad förståelse för hur teknisk infrastruktur formar innovationsförmåga i en starkt reglerad och konservativ bransch, och pekar på vikten av strategiska vägval i en tid präglad av snabb digitalisering
Exploring the Relationship Between Food Neophobia and Olfaction : Acceptance of Fruits and Vegetables and Odor Liking, Identification and Awareness in Swedish Children Aged 9-12 years
No full textIn recent years, interest in the connection between food neophobia and olfaction has increased within research, primarily focused on olfactory function and predominantly including adults or adolescents. However, children's reluctance to eat unfamiliar foods raises concern in many households and may be linked to olfactory factors beyond function. The overall aim of this thesis was to study odor perception in relation to food neophobia in school-aged children. More specifically, focus lay on the identification, liking, and awareness of odors and the acceptance of fruits and vegetables. The thesis is based on sensory and survey data collected from Swedish children aged 9–12 years (n = 126). Food odors may offer a new form of familiarizing exposure, as exposure to healthy foods has been shown to enhance liking and reduce food neophobia. To study the interaction between food neophobia and the awareness of food, social, and environmental odors, the Swedish ChiPSO questionnaire was developed. Additionally, a new set of food odorants for use in research with children was developed to explore food neophobia in relation to the identification and liking of fruit and vegetable odors. In contrast to previous studies with adults and adolescents, no connection was observed in the present sample between food neophobia and olfactory function. In this first study of the relationship between childhood food neophobia and odor awareness, no direct connection was observed. However, higher odor awareness was associated with a lower acceptance of vegetables. In addition, higher environmental odor awareness was associated with a lower ability to identify odors. This may suggest that some children struggle to develop familiarity with certain odors due to avoidant behaviors. In the present sample, a positive connection was observed between participants' fruit and vegetable odor identification scores and their liking of the same odors. This may suggest a link between odor familiarity and food liking. Also, a connection was observed between high fruit and vegetable odor liking and high overall liking of the corresponding fruits and vegetables, rated through a questionnaire and the sensory evaluation of food samples. This might suggest a connection between odor-liking and food-liking, possibly indicating familiarization with odors as a promising approach for increasing food liking. In conclusion, there appear to be differences in how children with and without food neophobia interact with and perceive odors. This dissertation provides valuable insights into developmental olfaction and food neophobia in children, which may serve as a foundation for future interventions and research
Phylogenetic and Environmental Distribution of NirB-Ammonifiers
No full textNitrate ammonification is important for soil nitrogen retention. Dissimilatory nitrate reduction to ammonia (DNRA, also known as nitrate/nitrite ammonification) can compete with denitrification for substrates, retaining nitrogen in the soil as ammonium. There are multiple enzymes in two families that play a crucial role in this processes. The gene distribution of NrfA and Onr enzymes has been intensively studied, but NirB,called Nit-6in fungi, has not been systematically studied. Studies show that NirB-ammonifiers could contribute to the global ammonium pools. Research about the diversity and environmental diversity of NirB-ammonifiers can provide a more precise understanding of their genetic potential, further helping assess the abundance of soil NirB-ammonifiers across terrestrial biomes and evaluate their role in global nitrogen retention. In this study, we used previously published NirB and Nit-6 sequences as seed to search for nirB and nit-6 genes in 105,500 bacterial and fungal genomes and 1,583 metagenomes. The results showed that genes were widely distributed in fungi andbacteria. The abundance of nirB gene was similar to that of nrfA and much higher than that of nit-6. Random forest models found that pH, moisture, soil C/N, and aluminum and iron concentrations had important effects on nirB gene abundance. This study demonstrated the widespread presence of NirB and Nit-6 as well as identified factors that control the fate of soil nitrate
Observation of the Charmonium Decay → in /→
No full textUsing (2712.4±14.3)×106 (3686) events collected with the BESIII detector at the BEPCII collider, the decay → in /→ is observed. We determine the product branching fraction ℬ(/→)×ℬ(→)=(5.23±0.26stat±0.30syst)×10−6. This result is consistent with the lattice QCD calculation (5.34 ±0.16) ×10−6 from HPQCD in 2023. By using the world-average values of ℬ(/→) and the total decay width of , the partial decay width Γ( →) is determined to be (11.30±0.56stat±0.66syst±1.14ref) keV, which deviates from the corresponding world-average value by 3.4.For complete list of authors see http://dx.doi.org/10.1103/PhysRevLett.134.181901</p
Interplay between large low-recombining regions and pseudo-overdominance in a plant genome
No full textTo what extent overdominance might contribute to the maintenance of genetic diversity within genomes is still an ongoing research question. Pseudo-overdominance created by the complementation of deleterious alleles in heterozygotes has recently become a subject of particular interest. Simulations and theory suggest that pseudo-overdominance may occur in low recombining regions. Here, we conduct a comprehensive investigation of large low-recombining (LLR) regions in cultivated populations of pearl millet, an outcrossing diploid African cereal. We examine seven large regions ranging from 5 to 88 Mb and six of them are pericentromeric. These LLR regions exhibit an excess of heterozygotes, a distinctive hallmark of overdominance. They display a tendency toward a higher diversity and a larger ratio of non-synonymous and deleterious variants. We conduct a more in-depth study of the largest 88 Mb region, identified on chromosome 3. Interestingly, haplotypes of this region have been introgressed from wild relatives. Using long read sequencing, we confirm their strong divergence and the presence of inversions across one of them. One of the haplotypes seems to be highly deleterious in the homozygous state. A total of 17% of the cultivated pearl millet genome exhibit a local population structure suggestive of overdominance or possibly pseudo-overdominance. Our empirical results contribute to the accumulation of knowledge, which will enhance our understanding of the potential role of overdominance or pseudo-overdominance in maintaining genetic diversity, particularly in low recombining regions
Identifying Stem Cell Niches in the Esophageal Epithelium
No full textBackground The esophageal epithelium undergoes rapid turnover, necessitating continuous self-renewal from proliferative basal cells. Prior murine studies from our lab identified spatially distinct expression patterns of Igfbp2 and Igfbp5, suggesting transcriptional heterogeneity along the esophageal axis. However, the possible heterogeneity within the epithelium is yet to be understood. Aims This study aimed to experimentally understand the heterogeneity within the murine esophageal epithelium and validate niche factors previously identified in silico as critical for esophageal epithelial homeostasis. Additionally, we sought to assess the functional impact of these factors on epithelial cell behavior using in vitro organoid culture systems. Materials & Methods Esophageal tissues from Igfbp2- and Igfbp5-CreERT2 mice were used for immunofluorescence and lineage tracing. Single epithelial cells were isolated and either directly seeded or sorted by reporter expression to generate organoids. Organoids were treated with signaling modulators and analyzed via microscopy, flow cytometry, and qPCR to assess proliferation, differentiation, and gene expression. Results Igfbp2-positive cells, mainly located in the folded region, were more proliferative than negative counterparts. Igfbp5 knockout reduced clone size, indicating a role in promoting proliferation. Treatment with the TGF-β receptor I inhibitor A8301 during early organoid formation enhanced organoid-forming efficiency. Conclusions Cells in the extended and folded region, marked by Igfbp5- and Igfbp2-expression, respectively, exhibit heterogeneity in terms of basal cell behavior. Functionally, IGFBP5 appears to affect clone expansion in vivo. TGF-β pathway inhibition promotes early organoid formation, highlighting its potential in modulating epithelial regeneration. These findings provide insight in understanding the heterogeneity of the esophagus.
A semi-mechanistic population pharmacokinetic-pharmacodynamic model to assess downstream drug-target effects on erythropoiesis
No full textErythropoiesis is a complex process that results in the production of erythrocytes from hematopoietic stem cells in the bone marrow. This work aimed to develop a population pharmacokinetic-pharmacodynamic (PKPD) model describing erythropoiesis and hemoglobin synthesis following bitopertin, an inhibitor of glycine transporter 1 (GlyT1), administration. Data from a Phase 1 clinical trial in 67 healthy subjects administered bitopertin (10, 30, or 60 mg) or placebo for 120 days were analyzed. Hematological assessments included erythrocyte and reticulocyte counts, immature reticulocyte fraction, hemoglobin concentration, and mean corpuscular hemoglobin. The proposed semi-mechanistic model, which leverages data and physiological knowledge, was found to adequately simultaneously describe the dose- and time-dependent changes in the biomarkers. The framework was used to illustrate the potential outcome of hypothetical drug-target interactions at distinct stages of erythropoiesis and hemoglobin synthesis, exemplifying its usefulness in a clinical setting
Comprehensive analysis of the microbial consortium in the culture of flagellate Monocercomonoides exilis
No full textMonocercomonoides exilis is a model species of the amitochondrial eukaryotic group Oxymonadida, which makes it a suitable organism for studying the consequences of mitochondrial loss. Although M. exilis has an endobiotic lifestyle, it can be cultured in vitro in polyxenic conditions alongside an uncharacterized prokaryotic community, while attempts to create axenic cultures have not been successful. In this study, we used metagenomic sequencing, transcriptomics, and metabolomics to characterize the microbial consortium that supports the growth of M. exilis. We assembled genomes for 24 bacterial species and identified at least 30 species in total. M. exilis accounted for less than 1.5% of the DNA reads, while bacterial species dominated the sequence data and shifted in abundance over time. Our metabolic reconstruction and differential gene expression analyses show that the bacterial community relies on organic carbon oxidation, fermentation, and hydrogen production, but does not engage in methanogenesis. We observed rapid depletion of amino acids, nucleotides, glyceraldehyde, lactate, fatty acids, and alcohols in the medium, indicating a reliance on external nutrient recycling. The nitrogen cycle in this community is incomplete, with limited nitrogen fixation and no ammonia oxidation. Despite detailed metabolic profiling, we did not find any direct biochemical connections between M. exilis and the prokaryotes. Several bacterial species produce siderophores to assist themselves and others in the community in acquiring iron. However, M. exilis does not appear to benefit directly from siderophore-mediated iron transport and lacks known iron uptake pathways. This indicates that M. exilis may rely indirectly on the iron metabolism of other bacteria through phagocytosis. Additionally, some bacteria synthesize polyamines like spermidine and phosphatidylcholine, which M. exilis may need but cannot produce on its own. As the culture ages, M. exilis shows changes in gene expression consistent with starvation responses, including the upregulation of carbohydrate storage pathways and processes related to exocytosis. These findings provide new insights into microbial interactions within xenic cultures and emphasize the complex nature of maintaining amitochondriate eukaryotes in vitro
