Experimental observation of curved light-cones in a quantum field simulator.

We investigate signal propagation in a quantum field simulator of the Klein-Gordon model realized by two strongly coupled parallel one-dimensional quasi-condensates. By measuring local phononic fields after a quench, we observe the propagation of correlations along sharp light-cone fronts. If the local atomic density is inhomogeneous, these propagation fronts are curved. For sharp edges, the propagation fronts are reflected at the system's boundaries. By extracting the space-dependent variation of the front velocity from the data, we find agreement with theoretical predictions based on curved geodesics of an inhomogeneous metric. This work extends the range of quantum simulations of nonequilibrium field dynamics in general space-time metrics.

Epidemic of parvovirus B19 and disease severity in pregnant people, Denmark, January to March 2024.

We report an epidemic of parvovirus B19 infections in Denmark during the first quarter of 2024, with a peak incidence 3.5 times higher than during the most recent epidemic in 2017. In total, 20.1% (130/648) of laboratory-confirmed cases were pregnant. Severe adverse outcomes were observed among 12.3% (16/130) of pregnant people and included foetal anaemia, foetal hydrops and miscarriage. Parvovirus B19 infection is not systematically monitored, but a national laboratory-based surveillance system is currently being established in Denmark.

Factors associated with the formation of SARS-CoV-2 case-clusters in Danish schools: a nationwide register-based observational study.

A register-based retrospective observational study was conducted to describe SARS-CoV-2 cases and case-clusters in schoolchildren of Danish primary and lower secondary schools and identify which factors were associated with the occurrence of case-clusters in schools. The study period was the autumn school semester 2021. Clusters were defined as three or more cases in a school-class level within 14 days. Descriptive analysis was carried out and multivariable logistic regression analysis was performed to determine which factors were associated with case introductions (i.e., primary case) being linked to a cluster. More cases and clusters were identified in lower than in higher class levels. Out of 21,497 cases introduced into a school, 41.6% started a cluster. A higher assumed immunity level in a class level was significantly reducing the odds of a case introduction being linked to a cluster (e.g., assumed immunity of ≥80% vs <20%: OR: 0.28; 95%CI: 0.17-0.44). A previous infection (in the primary case) had a protective effect (OR: 0.58; 95%CI: 0.33-0.99). This study suggests that most cases appearing in schools did not induce clusters, but that once cluster occur sizes can be large. It further indicates that vaccination of children markedly reduces the risk of secondary infections.

Surveillance of SARS-CoV-2 infection based on self-administered swabs, Denmark, May to July 2022: evaluation of a pilot study.

BackgroundDuring the COVID-19 pandemic, the Danish National Institute for Infectious Disease, Statens Serum Institute (SSI) developed a home-based SARS-CoV-2 surveillance system.AimsWe wanted to determine whether a cohort of individuals performing self-administered swabs for PCR at home could support surveillance of SARS-CoV-2, including detection and assessment of new variants. We also aimed to evaluate the logistical setup.MethodsFrom May to July 2022, 10,000 blood donors were invited to participate, along with their household members. Participation required performing a self-swab for 4 consecutive weeks and answering symptom questionnaires via a web app. Swabs were sent by post to SSI for PCR analysis and whole genome sequencing. After study completion, participants were asked to complete a questionnaire concerning their experience.ResultsIn total, 2,186 individuals enrolled (47.4% blood donors), and 1,333 performed self-swabbing (53.0 blood donors), of whom 48 had at least one SARS-CoV-2-positive sample. Fourteen different Omicron subvariants, primarily BA.5 subvariants, were identified by whole genome sequencing (WGS). In total, 29 of the 63 SARS-CoV-2-positive samples were taken from individuals who were asymptomatic at the time of swabbing. Participants collected 2.9 swabs on average, with varying intervals between swabs. Transmission within households was observed in only three of 25 households.ConclusionParticipants successfully performed self-swabs and answered symptom questionnaires. Also, WGS analysis of samples was possible. The system can support surveillance of respiratory pathogens and also holds potential as a diagnostic tool, easing access to test for at-risk groups, while also reducing the burden on healthcare system resources.

Antimicrobial resistance monitoring in the Danish swine production by phenotypic methods and metagenomics from 1999 to 2018.

BackgroundIn Denmark, antimicrobial resistance (AMR) in pigs has been monitored since 1995 by phenotypic approaches using the same indicator bacteria. Emerging methodologies, such as metagenomics, may allow novel surveillance ways.AimThis study aimed to assess the relevance of indicator bacteria (Escherichia coli and Enterococcus faecalis) for AMR surveillance in pigs, and the utility of metagenomics.MethodsWe collated existing data on AMR and antimicrobial use (AMU) from the Danish surveillance programme and performed metagenomics sequencing on caecal samples that had been collected/stored through the programme during 1999-2004 and 2015-2018. We compared phenotypic and metagenomics results regarding AMR, and the correlation of both with AMU.ResultsVia the relative abundance of AMR genes, metagenomics allowed to rank these genes as well as the AMRs they contributed to, by their level of occurrence. Across the two study periods, resistance to aminoglycosides, macrolides, tetracycline, and beta-lactams appeared prominent, while resistance to fosfomycin and quinolones appeared low. In 2015-2018 sulfonamide resistance shifted from a low occurrence category to an intermediate one. Resistance to glycopeptides consistently decreased during the entire study period. Outcomes of both phenotypic and metagenomics approaches appeared to positively correlate with AMU. Metagenomics further allowed to identify multiple time-lagged correlations between AMU and AMR, the most evident being that increased macrolide use in sow/piglets or fatteners led to increased macrolide resistance with a lag of 3-6 months.ConclusionWe validated the long-term usefulness of indicator bacteria and showed that metagenomics is a promising approach for AMR surveillance.

First cases of SARS-CoV-2 BA.2.86 in Denmark, 2023.

We describe 10 cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant BA.2.86 detected in Denmark, including molecular characteristics and results from wastewater surveillance that indicate that the variant is circulating in the country at a low level. This new variant with many spike gene mutations was classified as a variant under monitoring by the World Health Organization on 17 August 2023. Further global monitoring of COVID-19, BA.2.86 and other SARS-CoV-2 variants is highly warranted.

Floquet Engineering a Bosonic Josephson Junction.

We study Floquet engineering of the tunnel coupling between a pair of one-dimensional bosonic quasicondensates in a tilted double-well potential. By modulating the energy difference between the two wells, we reestablish tunnel coupling and precisely control its amplitude and phase. This allows us to initiate coherence between two initially uncorrelated Bose gases and prepare different initial states in the emerging sine-Gordon Hamiltonian. We fully characterize the Floquet system and study the dependence of both equilibrium properties and relaxation on the modulation.

Increased transmission of SARS-CoV-2 in Denmark during UEFA European championships.

Denmark hosted four games during the 2020 UEFA European championships (EC2020). After declining positive SARS-CoV-2 test rates in Denmark, a rise occurred during and after the tournament, concomitant with the replacement of the dominant Alpha lineage (B.1.1.7) by the Delta lineage (B.1.617.2), increasing vaccination rates and cessation of several restrictions. A cohort study including 33 227 cases was conducted from 30 May to 25 July 2021, 14 days before and after the EC2020. Included was a nested cohort with event information from big-screen events and matches at the Danish national stadium, Parken (DNSP) in Copenhagen, held from 12 June to 28 June 2021. Information from whole-genome sequencing, contact tracing and Danish registries was collected. Case-case connections were used to establish transmission trees. Cases infected on match days were compared to cases not infected on match days as a reference. The crude incidence rate ratio (IRR) of transmissions was 1.55, corresponding to 584 (1.76%) cases attributable to EC2020 celebrations. The IRR adjusted for covariates was lower (IRR 1.41) but still significant, and also pointed to a reduced number of transmissions from fully vaccinated cases (IRR 0.59). These data support the hypothesis that the EC2020 celebrations contributed to the rise of cases in Denmark in the early summer of 2021.

UK IBD Twin Registry: Concordance and Environmental Risk Factors of Twins with IBD.

BACKGROUND AND AIMS: Twin studies have long been used to infer heritability. Within the 'omics era, twin cohorts have even greater research potential. This study describes the formation of the UK IBD Twin Registry and analysis of concordance and environmental factors. METHOD: Twin pairs with IBD were recruited by advertising via IBD charities and social media, re-tracing a dormant IBD database and clinician referral. Details of zygosity, concordance, disease history and environmental factors were assessed. Pair concordance was calculated, and environmental factors were analysed with logistic regression models adjusted for zygosity and concordance. RESULTS: Ninety-one twin pairs were included in the analysis; forty-two with CD and forty-nine with UC. More MZ twin pairs with CD were concordant compared with DZ pairs, thus inferring heritability (Chi-sq. 15.6. P < 0.001). In UC, MZ concordance was also numerically greater. Cigarette smoking was predictive of CD (OR 2.66, 95% CI 1.16 to 6.07 P = 0.02); there may be an independent association with cannabis smoking (OR 2.59 95% CI 0.89 to 7.55 P = 0.08). Breastfeeding was protective against UC (OR 0.48, 95% CI 0.25-0.93, P = 0.03), but not CD. Self-reports of less occurrences of gastroenteritis than peers were protective against future UC onset (OR 0.33 95% CI 0.15 to 0.74, P = 0.01). Method of delivery, parental attitudes towards hygiene and recall of diet did not impact future IBD concordance. CONCLUSIONS: This study supports the heritability of IBD. Twin study analysis was able to elucidate environmental factors associated with IBD.

Nationwide study on SARS-CoV-2 transmission within households from lockdown to reopening, Denmark, 27 February 2020 to 1 August 2020.

BackgroundThe COVID-19 pandemic is one of the most serious global public health threats of recent times. Understanding SARS-CoV-2 transmission is key for outbreak response and to take action against the spread of disease. Transmission within the household is a concern, especially because infection control is difficult to apply within this setting.AimThe objective of this observational study was to investigate SARS-CoV-2 transmission in Danish households during the early stages of the COVID-19 pandemic.MethodsWe used comprehensive administrative register data from Denmark, comprising the full population and all COVID-19 tests from 27 February 2020 to 1 August 2020, to estimate household transmission risk and attack rate.ResultsWe found that the day after receiving a positive test result within the household, 35% (788/2,226) of potential secondary cases were tested and 13% (98/779) of these were positive. In 6,782 households, we found that 82% (1,827/2,226) of potential secondary cases were tested within 14 days and 17% (371/2,226) tested positive as secondary cases, implying an attack rate of 17%. We found an approximate linear increasing relationship between age and attack rate. We investigated the transmission risk from primary cases by age, and found an increasing risk with age of primary cases for adults (aged ≥ 15 years), while the risk seems to decrease with age for children (aged < 15 years).ConclusionsAlthough there is an increasing attack rate and transmission risk of SARS-CoV-2 with age, children are also able to transmit SARS-CoV-2 within the household.

Molecular epidemiology of the SARS-CoV-2 variant Omicron BA.2 sub-lineage in Denmark, 29 November 2021 to 2 January 2022.

Following emergence of the SARS-CoV-2 variant Omicron in November 2021, the dominant BA.1 sub-lineage was replaced by the BA.2 sub-lineage in Denmark. We analysed the first 2,623 BA.2 cases from 29 November 2021 to 2 January 2022. No epidemiological or clinical differences were found between individuals infected with BA.1 versus BA.2. Phylogenetic analyses showed a geographic east-to-west transmission of BA.2 from the Capital Region with clusters expanding after the Christmas holidays. Mutational analysis shows distinct differences between BA.1 and BA.2.

Extension of the Generalized Hydrodynamics to the Dimensional Crossover Regime.

In an effort to address integrability breaking in cold gas experiments, we extend the integrable hydrodynamics of the Lieb-Liniger model with two additional components representing the population of atoms in the first and second transverse excited states, thus enabling a description of quasi-1D condensates. Collisions between different components are accounted for through the inclusion of a Boltzmann-type collision integral in the hydrodynamic equation. Contrary to standard generalized hydrodynamics, our extended model captures thermalization of the condensate at a rate consistent with experimental observations from a quantum Newton's cradle setup.

Designing arbitrary one-dimensional potentials on an atom chip.

We use laser light shaped by a digital micro-mirror device to realize arbitrary optical dipole potentials for one-dimensional (1D) degenerate Bose gases of 87Rb trapped on an atom chip. Superposing optical and magnetic potentials combines the high flexibility of optical dipole traps with the advantages of magnetic trapping, such as effective evaporative cooling and the application of radio-frequency dressed state potentials. As applications, we present a 160 µm long box-like potential with a central tuneable barrier, a box-like potential with a sinusoidally modulated bottom and a linear confining potential. These potentials provide new tools to investigate the dynamics of 1D quantum systems and will allow us to address exciting questions in quantum thermodynamics and quantum simulations.

A Cost-Effective High-Throughput Plasma and Serum Proteomics Workflow Enables Mapping of the Molecular Impact of Total Pancreatectomy with Islet Autotransplantation.

Blood is an ideal body fluid for the discovery or monitoring of diagnostic and prognostic protein biomarkers. However, discovering robust biomarkers requires the analysis of large numbers of samples to appropriately represent interindividual variability. To address this analytical challenge, we established a high-throughput and cost-effective proteomics workflow for accurate and comprehensive proteomics at an analytical depth applicable for clinical studies. For validation, we processed 1 µL each from 62 plasma samples in 96-well plates and analyzed the product by quantitative data-independent acquisition liquid chromatography/mass spectrometry; the data were queried using feature quantification with Spectronaut. To show the applicability of our workflow to serum, we analyzed a unique set of samples from 48 chronic pancreatitis patients, pre and post total pancreatectomy with islet autotransplantation (TPIAT) surgery. We identified 16 serum proteins with statistically significant abundance alterations, which represent a molecular signature distinct from that of chronic pancreatitis. In summary, we established a cost-efficient high-throughput workflow for comprehensive proteomics using PVDF-membrane-based digestion that is robust, automatable, and applicable to small plasma and serum volumes, e.g., finger stick. Application of this plasma/serum proteomics workflow resulted in the first mapping of the molecular implications of TPIAT on the serum proteome.

Analysis of consumer food purchase data used for outbreak investigations, a review.

BackgroundInvestigations of food-borne outbreaks are frequently unsuccessful and new investigation methods should be welcomed. Aim: Describe the use of consumer purchase datasets in outbreak investigations and consider methodological and practical difficulties. Methods: We reviewed published papers describing the use of consumer purchase datasets, where electronic data on the foods that case-patients had purchased before onset of symptoms were obtained and analysed as part of outbreak investigations. Results: For the period 2006-17, scientific articles were found describing 20 outbreak investigations. Most outbreaks involved salmonella or Shiga toxin-producing Escherichia coli and were performed in eight different countries. The consumer purchase datasets were most frequently used to generate hypotheses about the outbreak vehicle where case-interviews had not been fruitful. Secondly, they were used to aid trace-back investigation, where a vehicle was already suspected. A number of methodological as well as (in some countries) legal and practical impediments exist. Conclusions: Several of the outbreaks were unlikely to have been solved without the use of consumer purchase datasets. The method is potentially powerful and with future improved access to big data purchase information, may become a widely applicable tool for outbreak investigations, enabling investigators to quickly find hypotheses and at the same time estimate odds ratios or relative risks hereof. We suggest using the term 'consumer purchase data' to refer to the approach in the future.

Familial risk of inflammatory bowel disease: a population-based cohort study 1977-2011.

OBJECTIVES: Estimates of familial risk of inflammatory bowel diseases (IBDs), Crohn's disease (CD), and ulcerative colitis (UC) are needed for counseling of patients and could be used to target future prevention. We aimed to provide comprehensive population-based estimates of familial risk of IBD. METHODS: The study encompassed the entire Danish population during 1977-2011 (N=8,295,773; 200 million person-years). From national registries, we obtained information on diagnosis date of IBD (N=45,780) and family ties. Using Poisson regression, we estimated incidence rate ratios (IRRs) of IBD in relatives of IBD cases compared with individuals with relatives of the same type without IBD. RESULTS: The risk of CD was significantly increased in first-degree (IRR, 7.77; 95% confidence interval (CI), 7.05-8.56), second-degree (IRR, 2.44; 95% CI, 2.01-2.96), and third-degree relatives (IRR, 1.88; 95% CI, 1.30-2.71) to patients with CD, and was less pronounced in relatives to UC cases. Likewise, the risk of UC was increased in first-degree (IRR, 4.08; 95% CI, 3.81-4.38), second-degree (IRR, 1.85; 95% CI, 1.60-2.13), and third-degree relatives (IRR, 1.51; 95% CI, 1.07-2.12) of UC cases, and less pronounced in relatives of CD cases. IRRs increased with two or more IBD-affected relatives and were modified by age, with the highest family-related IRR observed in early life. CONCLUSIONS: The risk of IBD is significantly increased in first -, second-, and third-degree relatives of IBD-affected cases, with up to 12% of all IBD cases being family cases. The risk is particularly pronounced in young individuals.

The first complete genome sequence of Staphylococcus aureus ST5477.

This study presents the first complete genome of Staphylococcus aureus ST5477, one of the most common sequence types (ST) from bovine in eastern Africa. The genome consists of a 2,723,132-bp circular chromosome and a 3,044-bp plasmid. This strain was collected in 2017 from cow milk in Tanzania.

Overweight in childhood and consumer purchases in a Danish cohort.

BACKGROUND: Prevention and management of childhood overweight involves the entire family. We aimed to investigate purchase patterns in households with at least one member with overweight in childhood by describing expenditure on different food groups. METHODS: This Danish register-based cohort study included households where at least one member donated receipts concerning consumers purchases in 2019-2021 and at least one member had their Body mass index (BMI) measured in childhood within ten years prior to first purchase. A probability index model was used to evaluate differences in proportion expenditure spent on specific food groups. RESULTS: We identified 737 households that included a member who had a BMI measurement in childhood, 220 with overweight and 517 with underweight or normal weight (reference households). Adjusting for education, income, family type, and urbanization, households with a member who had a BMI classified as overweight in childhood had statistically significant higher probability of spending a larger proportion of expenditure on ready meals 56.29% (95% CI: 51.70;60.78) and sugary drinks 55.98% (95% CI: 51.63;60.23). Conversely, they had a statistically significant lower probability of spending a larger proportion expenditure on vegetables 38.44% (95% CI: 34.09;42.99), compared to the reference households. CONCLUSION: Households with a member with BMI classified as overweight in childhood spent more on unhealthy foods and less on vegetables, compared to the reference households. This study highlights the need for household/family-oriented nutrition education and intervention.

Relative vaccine protection, disease severity, and symptoms associated with the SARS-CoV-2 omicron subvariant BA.2.86 and descendant JN.1 in Denmark: a nationwide observational study.

BACKGROUND: During the 2023 Danish COVID-19 vaccination campaign, an updated monovalent mRNA vaccine targeting the SARS-CoV-2 omicron XBB.1.5 subvariant was administered. However, the rapid spread of a genetically divergent omicron BA.2.86 subvariant, JN.1, since September, 2023, poses potential challenges due to its rapid dominance and possible immune escape. Using national electronic health registry data from all regions of Denmark, we aimed to investigate whether the SARS-CoV-2 subvariant BA.2.86, and its descendant JN.1, differed from other circulating variants in terms of their ability to escape vaccine protection, the risk of infection leading to severe disease, and self-reported symptoms among infected people. METHODS: In this observational study, we included all residents of Denmark aged 65 years and older who tested positive for SARS-CoV-2 by PCR between Oct 1 and Dec 31, 2023, and for whom genomic data on the SARS-CoV-2 variant that had caused their infection were available. Data from clinical testing, sentinel, and self-sampling-based surveillance were linked with national electronic civil, vaccination, and hospitalisation registers. The relative protection of the XBB.1.5 updated COVID-19 vaccine against BA.2.86 infections versus infections with other variants was analysed in a case-only study, and the relative risk of hospitalisation in people infected with BA.2.86 versus other variants was analysed in a case-control study. Both analyses were adjusted for time, comorbidities, and previous vaccination history, among other potential confounders. Additionally, prevalence patterns in self-reported symptoms among people of all ages infected with SARS-CoV-2 were reported separately by subvariant. FINDINGS: Of the 7581 people in Denmark aged 65 years or older who tested positive for SARS-CoV-2 by PCR during the study period, 5882 (78%) samples were eligible for sequencing. 3862 (66%) of these passed quality control, were successfully sequenced, and the SARS-CoV-2 variant and subvariant identified, and these individuals were included in the study. Of these 3862 people, 2184 (57%) were infected with the BA.2.86 subvariant, including 1615 JN.1 infections. Participants infected with BA.2.86 had 1·52 (95% CI 1·25-1·86) times the odds, and those infected with JN.1 had 1·60 (1·27-2·02) times the odds, of having received the XBB.1.5 vaccine at least 7 days before their infection compared with participants infected with a non-BA.2.86 variant. The severity analysis showed no evidence of association between the infecting variant and the risk of COVID-19 hospitalisation (odds ratio 1·04 [95% CI 0·86-1·26] for BA.2.86 and 1·07 [0·85-1·34] for JN.1). Similarly, there was no evidence of differences in self-reported symptoms by variant strain. INTERPRETATION: Compared with other SARS-CoV-2 variants, BA.2.86 and the JN.1 sublineage were less sensitive to vaccine-induced immune protection from the XBB.1.5 updated COVID-19 vaccine; however, we found no evidence that infection with BA.2.86 or JN.1 resulted in increased disease severity or different symptom profiles. Although less effective against the new variants, XBB.1.5 vaccination remains protective and reduces the risk of infection and COVID-19 disease. FUNDING: The Danish Government and the EU's EU4Health programme.

Cohort profile: The Health, Food, Purchases and Lifestyle (SMIL) cohort - a Danish open cohort.

PURPOSE: The Health, Food, Purchases and Lifestyle (SMIL) cohort is a prospective open Danish cohort that collects electronic consumer purchase data, which can be linked to Danish nationwide administrative health and social registries. This paper provides an overview of the cohort's baseline characteristics and marginal differences in the monetary percentage spent on food groups by sex, age and hour of the day. PARTICIPANTS: As of 31 December 2022, the cohort included 11 214 users of a smartphone-based receipt collection application who consented to share their unique identification number for linkage to registries in Denmark. In 2022, the composition of the cohort was as follows: 62% were men while 24% were aged 45-55. The cohort had a median of 63 (IQR 26-116) unique shopping trips. The cohort included participants with a range of health statuses. Notably, 21% of participants had a history of cardiovascular disease and 8% had diabetes before donating receipts. FINDINGS TO DATE: The feasibility of translating consumer purchase data to operationalisable food groups and merging with registers has been demonstrated. We further demonstrated differences in marginal distributions which revealed disparities in the amount of money spent on various food groups by sex and age, as well as systematic variations by the hour of the day. For example, men under 30 spent 8.2% of their total reported expenditure on sugary drinks, while women under 30 spent 6.5%, men over 30 spent 4.3% and women over 30 spent 3.9%. FUTURE PLANS: The SMIL cohort is characterised by its dynamic, continuously updated database, offering an opportunity to explore the relationship between diet and disease without the limitations of self-reported data. Currently encompassing data from 2018 to 2022, data collection is set to continue. We expect data collection to continue for many years and we are taking several initiatives to increase the cohort.