Abstract Genotyping is a core application of high-throughput sequencing. We present KAGE, a genotyper for SNPs and short indels that is inspired by recent developments within graph-based genome representations and alignment-free methods. KAGE uses a pan-genome representation of the population to efficiently and accurately predict genotypes. Two novel ideas improve both the speed and accuracy: a Bayesian model incorporates genotypes from thousands of individuals to improve prediction accuracy, and a computationally efficient method leverages correlation...

Abstract Oslo, the capital of Norway, is situated in a North European cool climate zone. We investigate the effect of weather on the overall level of crime in the city, as well as the impact of different aspects of weather (temperature, wind speed, precipitation) on the spatial distribution of crime, net of both total level of crime, time of day and seasonality. Geocoded locations of criminal offences were combined with data on temperature, wind speed,...

Understanding the historical emergence and growth of long-range fisheries can provide fundamental insights into the timing of ecological impacts and the development of coastal communities during the last millennium. Whole-genome sequencing approaches can improve such understanding by determining the origin of archaeological fish specimens that may have been obtained from historic trade or distant water. Here, we used genome-wide data to individually infer the biological source of 37 ancient Atlantic cod specimens (ca 1050–1950 CE)...

Abstract Background Since viral metagenomic approach was applied to discover plant viruses for the first time in 2006, many plant viruses had been identified from cultivated and non-cultivated plants. These previous researches exposed that the viral communities (virome) of plants have still largely uncharacterized. Here, we investigated the virome in 161 species belonging to 38 plant orders found in a riverside ecosystem. Results We identified 245 distinct plant-associated virus genomes (88 DNA and 157 RNA...

Abstract Objective To compare colorectal cancer (CRC) incidences in carriers of pathogenic variants of the MMR genes in the PLSD and IMRC cohorts, of which only the former included mandatory colonoscopy surveillance for all participants. Methods CRC incidences were calculated in an intervention group comprising a cohort of confirmed carriers of pathogenic or likely pathogenic variants in mismatch repair genes (path_MMR) followed prospectively by the Prospective Lynch Syndrome Database (PLSD). All had colonoscopy surveillance, with...

Abstract Gaining knowledge of what contextual factors may contribute to changes in student achievement across cycles of international large-scale assessments (ILSA), is important for educational policy and practice. Addressing this necessitates advanced methodology that utilizes the trend design of the ILSAs. The Trends in International Mathematics and Science Study (TIMSS) data is suitable for such analyses as it measures students’ competence based on the participating countries curricula. In Norway, students’ performance in mathematics decreased from...

Abstract Background Good health decisions depend on one’s ability to think critically about health claims and make informed health choices. Young people can learn these skills through school-based interventions, but learning resources need to be low-cost and built around lessons that can fit into existing curricula. As a first step to developing and evaluating digital learning resources that are feasible to use in Kenyan secondary schools, we conducted a context analysis to explore interest in...

IntroductionADAMTS13 cleaves von Willebrand factor (VWF) multimers into less active fragments. Both markers have been related to cardiovascular disease (CVD). We aimed to investigate the influence of ADAMTS13 single nucleotide polymorphisms (SNPs) on levels of ADAMTS13 and VWF, and CVD.MethodsThe c.1342C>G, g.41635A>G and c.2699C>T polymorphisms were determined in patients with chronic coronary syndrome (n = 1000). VWF and ADAMTS13 were analyzed. Clinical endpoints after 2 years (n = 106) were unstable angina pectoris, myocardial infarction,...

Abstract Background Several modifiable lifestyle risk factors for dementia have been identified, but it is unclear how much the Norwegian public knows about the relationship between lifestyle and brain health. Therefore, this study aimed to investigate knowledge about modifiable dementia risk and protective factors and beliefs and attitudes towards dementia and dementia risk reduction in a randomly selected subsample of the Norwegian population. Methods The total sample (n = 1435) included individuals aged 40–70 years...

Abstract Background Knowledge on healthcare utilization after mass trauma is needed to strengthen the public health preparedness to such incidents. Using register-based data, this study had a unique opportunity to investigate how young survivors’ use of primary care physicians (PCP) and mental health services (MHS) changed after a terrorist attack. Methods We examined register-based data on PCP and MHS consultations among 255 survivors (52% male) of the 2011 Utøya youth camp attack in Norway 3...

Abstract Background Mitochondrial dysfunction is a hallmark of both critical illness and propofol infusion syndrome and its severity seems to be proportional to the doses of noradrenaline, which patients are receiving. We comprehensively studied the effects of noradrenaline on cellular bioenergetics and mitochondrial biology in human skeletal muscle cells with and without propofol-induced mitochondrial dysfunction. Methods Human skeletal muscle cells were isolated from vastus lateralis biopsies from patients undergoing elective hip replacement surgery (n =...

Abstract Background Cardiac troponin T (cTnT) is a biomarker of myocardial injury frequently elevated in COPD patients, potentially because of hypoxemia. This non-randomised observational study investigates whether long-term oxygen treatment (LTOT) reduces the cTnT level. Methods We compared cTnT between COPD patients who were candidates for LTOT (n = 20) with two reference groups. Patients from both reference groups were matched with the index group using propensity score.Reference groups consists of institutional pulmonary rehabilitation patients...

Abstract Background The objective of the study was to investigate variability and agreement of the commonly used image processing method “n-SD from remote” and in particular for quantifying myocardial infarction by late gadolinium enhancement (LGE) cardiovascular magnetic resonance (CMR). LGE-CMR in tandem with the analysis method “n-SD from remote” represents the current reference standard for infarct quantification. This analytic method utilizes regions of interest (ROIs) and defines infarct as the tissue with a set number...

Abstract Background In regard to health service planning and delivery, the use of information at different levels in the health system is vital, ranging from the influencing of policy to the programming of action to the ensuring of evidence-informed practices. However, neither ownership of, nor access to, good quality data guarantees actual use of these data. For information to be used, relevant data need to be collected, processed and analysed in an accessible format. This...

Abstract Background L-tryptophan (Trp) metabolism involved in mediating tumour development and immune suppression. However, comprehensive analysis of the role of the Trp metabolism pathway is still a challenge. Methods We downloaded Trp metabolism-related genes’ expression data from different public databases, including TCGA, Gene Expression Omnibus (GEO) and Hepatocellular Carcinoma Database (HCCDB). And we identified two metabolic phenotypes using the ConsensusClusterPlus package. Univariate regression analysis and lasso Cox regression analysis were used to establish a risk...

Abstract Background To optimize colorectal cancer (CRC) screening and surveillance, information regarding the time-dependent risk of advanced adenomas (AA) to develop into CRC is crucial. However, since AA are removed after diagnosis, the time from AA to CRC cannot be observed in an ethically acceptable manner. We propose a statistical method to indirectly infer this time in a progressive three-state disease model using surveillance data. Methods Sixteen models were specified, with and without covariates. Parameters...

Abstract Background L-tryptophan (Trp) metabolism involved in mediating tumour development and immune suppression. However, comprehensive analysis of the role of the Trp metabolism pathway is still a challenge. Methods We downloaded Trp metabolism-related genes’ expression data from different public databases, including TCGA, Gene Expression Omnibus (GEO) and Hepatocellular Carcinoma Database (HCCDB). And we identified two metabolic phenotypes using the ConsensusClusterPlus package. Univariate regression analysis and lasso Cox regression analysis were used to establish a risk...

Abstract Background Suboptimal medication use contributes to a substantial proportion of hospitalizations and emergency department visits in older adults. We designed a clinical pharmacist intervention to optimize medication therapy in older hospitalized patients. Based on the integrated medicine management (IMM) model, the 5-step IMMENSE intervention comprise medication reconciliation, medication review, reconciled medication list upon discharge, patient counselling, and post discharge communication with primary care. The objective of this study was to evaluate the effects of...

Abstract Background In 2011 Norway granted undocumented women the right to antenatal care and to give birth at a hospital but did not include them in the general practitioner and reimbursement schemes. As a response to limited access to health care, Non-Governmental Organizations (NGO) have been running health clinics for undocumented migrants in Norway’s two largest cities. To further facilitate universal health coverage, there is a need to investigate how pregnant undocumented women use NGO...

Abstract Background To optimize colorectal cancer (CRC) screening and surveillance, information regarding the time-dependent risk of advanced adenomas (AA) to develop into CRC is crucial. However, since AA are removed after diagnosis, the time from AA to CRC cannot be observed in an ethically acceptable manner. We propose a statistical method to indirectly infer this time in a progressive three-state disease model using surveillance data. Methods Sixteen models were specified, with and without covariates. Parameters...

Abstract Background To optimize colorectal cancer (CRC) screening and surveillance, information regarding the time-dependent risk of advanced adenomas (AA) to develop into CRC is crucial. However, since AA are removed after diagnosis, the time from AA to CRC cannot be observed in an ethically acceptable manner. We propose a statistical method to indirectly infer this time in a progressive three-state disease model using surveillance data. Methods Sixteen models were specified, with and without covariates. Parameters...

Abstract Background In regard to health service planning and delivery, the use of information at different levels in the health system is vital, ranging from the influencing of policy to the programming of action to the ensuring of evidence-informed practices. However, neither ownership of, nor access to, good quality data guarantees actual use of these data. For information to be used, relevant data need to be collected, processed and analysed in an accessible format. This...

Abstract Oslo, the capital of Norway, is situated in a North European cool climate zone. We investigate the effect of weather on the overall level of crime in the city, as well as the impact of different aspects of weather (temperature, wind speed, precipitation) on the spatial distribution of crime, net of both total level of crime, time of day and seasonality. Geocoded locations of criminal offences were combined with data on temperature, wind speed,...

Abstract Background The durability of vaccine-induced humoral immunity against SARS-CoV-2 in patients with immune-mediated inflammatory diseases (IMIDs) on immunosuppressive therapy is not known. The aim of this study was to compare the persistence of anti-Spike antibodies following two-dose SARS-CoV-2 vaccination between IMID patients and healthy controls and to identify factors associated with antibody decline. Methods IMID patients on immunosuppressive medication enrolled in the prospective observational Nor-vaC study were included. Participants received two-dose SARS-CoV-2 vaccination. Serum...

Abstract Background The durability of vaccine-induced humoral immunity against SARS-CoV-2 in patients with immune-mediated inflammatory diseases (IMIDs) on immunosuppressive therapy is not known. The aim of this study was to compare the persistence of anti-Spike antibodies following two-dose SARS-CoV-2 vaccination between IMID patients and healthy controls and to identify factors associated with antibody decline. Methods IMID patients on immunosuppressive medication enrolled in the prospective observational Nor-vaC study were included. Participants received two-dose SARS-CoV-2 vaccination. Serum...