Graph neural networks for crystal structures typically use the atomic positions and the atomic species as input. Unfortunately, this information is not available when predicting new materials, for which the precise geometrical information is unknown. We circumvent this problem by replacing the precise bond distances with embeddings of graph distances. This allows our networks to be applied directl

The improvements in GPU hardware, including hardware-accelerated ray tracing, and the push for fully dynamic realistic-looking video games, has been driving more research in the use of ray tracing in real-time applications. The work described in this thesis covers multiple aspects such as optimisations, adapting existing offline methods to real-time constraints, and adding effects which were hard

Presentation av EU-medlemstaters samt Norges privatkopieringsersättningsystem (private copying levy system) vid seminariet Nordisk utblick – vad kan Sverige lära angående ersättning för privatkopiering arrangerat av ElektronikBranschen den 2 juli 2018 i Visby, Gotland. http://program.almedalsveckan.info/53118

We present Bioconda (https://bioconda.github.io), a distribution of bioinformatics software for the lightweight, multi-platform and language-agnostic package manager Conda. Currently, Bioconda offers a collection of over 3000 software packages, which is continuously maintained, updated, and extended by a growing global community of more than 200 contributors. Bioconda improves analysis reproducibi

A high quality benchmark for small variants encompassing 88 to 90% of the reference genome has been developed for seven Genome in a Bottle (GIAB) reference samples. However a reliable benchmark for large indels and structural variants (SVs) is yet to be defined. In this study, we manually curated 1235 SVs which can ultimately be used to evaluate SV callers ortrain machine learning models. We devel

Maternal vaccination, resulting in transfer of protective IgG across the placenta, represents a promising strategy to prevent neonatal disease caused by group B Streptococcus (GBS). The prototype vaccine GBS-NN, a fusion protein consisting of the N-terminal domains of the alpha-like protein (Alp) family members AlphaC and Rib, has been shown to display a good safety profile and to elicit a strong

The precisionFDA Truth Challenge V2 aimed to assess the state-of-the-art of variant calling in difficult-to-map regions and the Major Histocompatibility Complex (MHC). Starting with FASTQ files, 20 challenge participants applied their variant calling pipelines and submitted 64 variant callsets for one or more sequencing technologies (~35X Illumina, ~35X PacBio HiFi, and ~50X Oxford Nanopore Techno

Light field microscopy (LFM) has emerged as a powerful tool for fast volumetric image acquisition in biology, but its effective throughput and widespread use has been hampered by a computationally demanding and artefact-prone image reconstruction process. Here, we present a novel framework consisting of a hybrid light-field light-sheet microscope and deep learning-based volume reconstruction, wher

Understanding how hematopoietic stem and progenitor cells (HSPCs) are regulated is of central importance for the development of new therapies for blood disorders and stem cell transplantation. To date, HSPC regulation has been extensively studied in vitro and in animal models, but less is known about the mechanisms in vivo in humans. Here, in a genome-wide association study on 13,167 individuals,

BACKGROUND: From the beginning of COVID-19 pandemic, pregnant women have been considered at greater risk of severe morbidity and mortality. However, data on hospitalized pregnant women show that the symptom profile and risk factors for severe disease are similar to those among women who are not pregnant, although preterm birth, Cesarean delivery, and stillbirth may be more frequent and vertical tr

Incidence of differentiated thyroid carcinoma (DTC) varies considerably between ethnic groups, with particularly high incidence rates in Pacific Islanders. Here, we conducted a genome-wide association study (GWAS) involving 1,554 cases/1,973 controls of European ancestry and 301 cases/348 controls of Oceanian ancestry from the EPITHYR consortium. Our results confirmed the association with the know

We performed the largest genome-wide meta-analysis (GWAMA) (Max N=26,494) of the levels of 184 cardiovascular-related plasma protein levels to date and reported 592 independent loci (pQTL) associated with the level of at least one protein (1308 significant associations, median 6 per protein). We estimated that only between 8-37% of testable pQTL overlap with established expression quantitative tra

Severe COVID-19 is characterised by immunopathology and epithelial injury. Proteomic studies have identified circulating proteins that are biomarkers of severe COVID-19, but cannot distinguish correlation from causation. To address this, we performed Mendelian randomisation (MR) to identify proteins that mediate severe COVID-19. Using protein quantitative trait loci (pQTL) data from the SCALLOP co

Background Vaccine effectiveness against COVID-19 needs to be assessed in diverse real-world population settings.Methods A cohort study of 805 741 residents in Skåne county, Southern Sweden, aged 18-64 years, of whom 26 587 received at least one dose of the BNT162b2 vaccine. Incidence rates of COVID-19 were estimated in sex- and age-adjusted analysis and stratified in two-week periods with substan

The overall aim of this PhD thesis was to investigate sedimentary micro-environments and ecosystemfunctioning of two coastal areas. We combined different high spatial resolution methods and multivariate analyses atdifferent spatio-temporal scales to reveal interactions between benthic faunal and geochemical compartments. Firstly,we investigated two stations with contrasted oxygen, nitrate and mang