| 1. |
|
|
| 2. |
- Sherratt, K., et al.
(författare)
-
Predictive performance of multi-model ensemble forecasts of COVID-19 across European nations
- 2023
-
Ingår i: eLIFE. - : eLife Sciences Publications Ltd. - 2050-084X. ; 12
-
Tidskriftsartikel (refereegranskat)abstract
- Methods: We used open-source tools to develop a public European COVID-19 Forecast Hub. We invited groups globally to contribute weekly forecasts for COVID-19 cases and deaths reported by a standardised source for 32 countries over the next 1–4 weeks. Teams submitted forecasts from March 2021 using standardised quantiles of the predictive distribution. Each week we created an ensemble forecast, where each predictive quantile was calculated as the equally-weighted average (initially the mean and then from 26th July the median) of all individual models’ predictive quantiles. We measured the performance of each model using the relative Weighted Interval Score (WIS), comparing models’ forecast accuracy relative to all other models. We retrospectively explored alternative methods for ensemble forecasts, including weighted averages based on models’ past predictive performance.Results: Over 52 weeks, we collected forecasts from 48 unique models. We evaluated 29 models’ forecast scores in comparison to the ensemble model. We found a weekly ensemble had a consistently strong performance across countries over time. Across all horizons and locations, the ensemble performed better on relative WIS than 83% of participating models’ forecasts of incident cases (with a total N=886 predictions from 23 unique models), and 91% of participating models’ forecasts of deaths (N=763 predictions from 20 models). Across a 1–4 week time horizon, ensemble performance declined with longer forecast periods when forecasting cases, but remained stable over 4 weeks for incident death forecasts. In every forecast across 32 countries, the ensemble outperformed most contributing models when forecasting either cases or deaths, frequently outperforming all of its individual component models. Among several choices of ensemble methods we found that the most influential and best choice was to use a median average of models instead of using the mean, regardless of methods of weighting component forecast models.Conclusions: Our results support the use of combining forecasts from individual models into an ensemble in order to improve predictive performance across epidemiological targets and populations during infectious disease epidemics. Our findings further suggest that median ensemble methods yield better predictive performance more than ones based on means. Our findings also highlight that forecast consumers should place more weight on incident death forecasts than incident case forecasts at forecast horizons greater than 2 weeks.
|
|
| 3. |
- Verra, L., et al.
(författare)
-
Controlled Growth of the Self-Modulation of a Relativistic Proton Bunch in Plasma
- 2022
-
Ingår i: Physical Review Accelerators and Beams. - : American Physical Society. - 2469-9888. ; 25:7
-
Tidskriftsartikel (refereegranskat)abstract
- A long, narrow, relativistic charged particle bunch propagating in plasma is subject to the self -modulation (SM) instability. We show that SM of a proton bunch can be seeded by the wakefields driven by a preceding electron bunch. SM timing reproducibility and control are at the level of a small fraction of the modulation period. With this seeding method, we independently control the amplitude of the seed wakefields with the charge of the electron bunch and the growth rate of SM with the charge of the proton bunch. Seeding leads to larger growth of the wakefields than in the instability case.
|
|
| 4. |
- Verra, L., et al.
(författare)
-
Development of the self-modulation instability of a relativistic proton bunch in plasma
- 2023
-
Ingår i: Physics of Plasmas. - : American Institute of Physics (AIP). - 1070-664X .- 1089-7674. ; 30:8
-
Tidskriftsartikel (refereegranskat)abstract
- Self-modulation is a beam-plasma instability that is useful to drive large-amplitude wakefields with bunches much longer than the plasma skin depth. We present experimental results showing that, when increasing the ratio between the initial transverse size of the bunch and the plasma skin depth, the instability occurs later along the bunch, or not at all, over a fixed plasma length because the amplitude of the initial wakefields decreases. We show cases for which self-modulation does not develop, and we introduce a simple model discussing the conditions for which it would not occur after any plasma length. Changing bunch size and plasma electron density also changes the growth rate of the instability. We discuss the impact of these results on the design of a particle accelerator based on the self-modulation instability seeded by a relativistic ionization front, such as the future upgrade of the Advanced WAKefield Experiment.
|
|
| 5. |
- Nechaeva, T., et al.
(författare)
-
Hosing of a Long Relativistic Particle Bunch in Plasma
- 2024
-
Ingår i: Physical Review Letters. - : American Physical Society. - 0031-9007 .- 1079-7114. ; 132:7
-
Tidskriftsartikel (refereegranskat)abstract
- Experimental results show that hosing of a long particle bunch in plasma can be induced by wakefields driven by a short, misaligned preceding bunch. Hosing develops in the plane of misalignment, selfmodulation in the perpendicular plane, at frequencies close to the plasma electron frequency, and are reproducible. Development of hosing depends on misalignment direction, its growth on misalignment extent and on proton bunch charge. Results have the main characteristics of a theoretical model, are relevant to other plasma -based accelerators and represent the first characterization of hosing.
|
|
| 6. |
- Strakova, A., et al.
(författare)
-
Recurrent horizontal transfer identifies mitochondrial positive selection in a transmissible cancer
- 2020
-
Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 11
-
Tidskriftsartikel (refereegranskat)abstract
- Autonomous replication and segregation of mitochondrial DNA (mtDNA) creates the potential for evolutionary conflict driven by emergence of haplotypes under positive selection for 'selfish' traits, such as replicative advantage. However, few cases of this phenomenon arising within natural populations have been described. Here, we survey the frequency of mtDNA horizontal transfer within the canine transmissible venereal tumour (CTVT), a contagious cancer clone that occasionally acquires mtDNA from its hosts. Remarkably, one canine mtDNA haplotype, A1d1a, has repeatedly and recently colonised CTVT cells, recurrently replacing incumbent CTVT haplotypes. An A1d1a control region polymorphism predicted to influence transcription is fixed in the products of an A1d1a recombination event and occurs somatically on other CTVT mtDNA backgrounds. We present a model whereby 'selfish' positive selection acting on a regulatory variant drives repeated fixation of A1d1a within CTVT cells.
|
|
| 7. |
- Dawson, Deborah A., et al.
(författare)
-
New methods to identify conserved microsatellite loci and develop primer sets of high cross-species utility - as demonstrated for birds
- 2010
-
Ingår i: Molecular Ecology Resources. - : Wiley. - 1755-098X .- 1755-0998. ; 10:3, s. 475-494
-
Tidskriftsartikel (refereegranskat)abstract
- We have developed a new approach to create microsatellite primer sets that have high utility across a wide range of species. The success of this method was demonstrated using birds. We selected 35 avian EST microsatellite loci that had a high degree of sequence homology between the zebra finch Taeniopygia guttata and the chicken Gallus gallus and designed primer sets in which the primer bind sites were identical in both species. For 33 conserved primer sets, on average, 100% of loci amplified in each of 17 passerine species and 99% of loci in five non-passerine species. The genotyping of four individuals per species revealed that 24-76% (mean 48%) of loci were polymorphic in the passerines and 18-26% (mean 21%) in the non-passerines. When at least 17 individuals were genotyped per species for four Fringillidae finch species, 71-85% of loci were polymorphic, observed heterozygosity was above 0.50 for most loci and no locus deviated significantly from Hardy-Weinberg proportions. This new set of microsatellite markers is of higher cross-species utility than any set previously designed. The loci described are suitable for a range of applications that require polymorphic avian markers, including paternity and population studies. They will facilitate comparisons of bird genome organization, including genome mapping and studies of recombination, and allow comparisons of genetic variability between species whilst avoiding ascertainment bias. The costs and time to develop new loci can now be avoided for many applications in numerous species. Furthermore, our method can be readily used to develop microsatellite markers of high utility across other taxa.
|
|
| 8. |
- Lakhani, Krupa, et al.
(författare)
-
Dissociation of air pollutants on the uniform surface of pentagonal BeP2
- 2021
-
Ingår i: Applied Surface Science. - : Elsevier. - 0169-4332 .- 1873-5584. ; 570
-
Tidskriftsartikel (refereegranskat)abstract
- In this present work, the investigation was carried out using density functional theory (DFT) for the dissociation of noxious gas molecules such as carbon and nitrogen-based molecules (CO, CO2, N-2, NH3, NO, and NO2) on a pentagonal two-dimensional beryllium diphosphide (BeP2). The pentagonal BeP2 monolayer has a similar band structure as graphene. Here, some carbon and nitrogen-based noxious gases such as CO, CO2, N-2, NH3, NO, and NO2 with Van der Waals (vdW) interaction behave like physisorbed, while strong covalent (Be-O) interactions of O-2 on BeP2 formed chemisorption. Due to the chemisorption of O-2 gas molecules, the bandgap at Dirac point at P-site on BeP2 opens. While CO, CO2, N-2, NO, and NO2 are dissociated at the C-site, only CO, N-2, and NO are dissociated at the P-site. Beryllium diphosphide's band-gap shifts resulting from interactions with CO, N-2, and O-2 molecules are just 6%, 12.1%, and 22.2%, respectively, meaning that the BeP2 material has a moderate and high sensitivity towards CO, N-2, and O-2 molecules. BeP2 appears to be a potential catalyst for the dissociation of CO, CO2, N-2, NO, NO2, and O-2 gas molecules, which is even more interesting.
|
|
| 9. |
- Meziane, El Kahina, et al.
(författare)
-
Bi-Functional Chicken Immunoglobulin-Like Receptors With a Single Extracellular Domain (ChIR-AB1): Potential Framework Genes Among a Relatively Stable Number of Genes Per Haplotype
- 2019
-
Ingår i: Frontiers in Immunology. - : FRONTIERS MEDIA SA. - 1664-3224. ; 10
-
Tidskriftsartikel (refereegranskat)abstract
- The leukocyte receptor complex (LRC) in humans encodes many receptors with immunoglobulin-like (Ig-like) extracellular domains, including the killer Ig-like receptors (KIRs) expressed on natural killer (NK) cells among others, the leukocyte Ig-like receptors (LILRs) expressed on myeloid and B cells, and an Fc receptor (FcR), all of which have important roles in the immune response. These highly-related genes encode activating receptors with positively-charged residues in the transmembrane region, inhibitory receptors with immuno-tyrosine based motifs (ITIMs) in the cytoplasmic tail, and bi-functional receptors with both. The related chicken Ig-like receptors (ChIRs) are almost all found together on a microchromosome, with over 100 activating (A), inhibitory (B), and bi-functional (AB) genes, bearing either one or two extracellular Ig-like domains, interspersed over 500-1,000 kB in the genome of an individual chicken. Sequencing studies have suggested rapid divergence and little overlap between ChIR haplotypes, so we wished to begin to understand their genetics. We chose to use a hybridization technique, reference strand-mediated conformational analysis (RSCA), to examine the ChIR-AB1 family, with a moderate number of genes dispersed across the microchromosome. Using fluorescently-labeled references (FLR), we found that RSCA and sequencing of ChIR-AB1 extracellular exon gave two groups of peaks with mobility correlated with sequence relationship to the FLR. We used this system to examine widely-used and well-characterized experimental chicken lines, finding only one or a few simple ChIR haplotypes for each line, with similar numbers of peaks overall. We found much more complicated patterns from a broiler line from a commercial breeder and a flock of red junglefowl, but trios of parents and offspring from another commercial chicken line show that the complicated patterns are due to heterozygosity, indicating a relatively stable number of peaks within haplotypes of these birds. Some ChIR-AB1 peaks were found in all individuals from the commercial lines, and some of these were shared with red junglefowl and the experimental lines derived originally from egg-laying chickens. Overall, this analysis suggests that there are some simple features underlying the apparent complexity of the ChIR locus.
|
|
| 10. |
|
|
| 11. |
- Siedlecka, A, et al.
(författare)
-
A relationship between carbonic anhydrase and rubisco in response to moderate cadmium stress during light activation of photosynthesis
- 1999
-
Ingår i: Zeitschrift für Naturforschung C - A Journal of Biosciences. - 0939-5075 .- 1865-7125. ; 54:9-10, s. 759-763
-
Tidskriftsartikel (refereegranskat)abstract
- In our previous research, we showed that low Cd concentration increases the effectiveness of the process es leading to activation of ribulose-1,5-bisphosphate carboxylase/oxygen ase (Rubisco). This stimulation was dependent on carbonic anhydrase (CA) activity and resulted in protecting Rubisco activity against Cd toxicity. The aim of the present paper was to test whether this mechanism has any influence on light activation of photosynthesis during the first 2 h of illumination. Both the "activation mechanism" of plant response to Cd-stress conditions and its full efficiency at low Cd concentration were confirmed. The CA-dependent light activation of Rubisco at low Cd level was correlated with accelerated attaining of the maximum Rubisco activity by these plants. The amount of Rubisco was also Cd- and time-dependent and varied from continuous accumulation in control plants till reaching the maximum level within 30 minutes for the high Cd concentration. An increase in CA activity that was found to be parallel to the decrease of the amount of CA suggested activation of the enzyme by low Cd concentration.
|
|
| 12. |
- Speakman, John R., et al.
(författare)
-
Total daily energy expenditure has declined over the past three decades due to declining basal expenditure, not reduced activity expenditure
- 2023
-
Ingår i: Nature Metabolism. - : NATURE PORTFOLIO. - 2522-5812. ; 5:4, s. 579-588
-
Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Obesity is caused by a prolonged positive energy balance(1,2). Whether reduced energy expenditure stemming from reduced activity levels contributes is debated(3,4). Here we show that in both sexes, total energy expenditure (TEE) adjusted for body composition and age declined since the late 1980s, while adjusted activity energy expenditure increased over time. We use the International Atomic Energy Agency Doubly Labelled Water database on energy expenditure of adults in the United States and Europe (n = 4,799) to explore patterns in total (TEE: n = 4,799), basal (BEE: n = 1,432) and physical activity energy expenditure (n = 1,432) over time. In males, adjusted BEE decreased significantly, but in females this did not reach significance. A larger dataset of basal metabolic rate (equivalent to BEE) measurements of 9,912 adults across 163 studies spanning 100 years replicates the decline in BEE in both sexes. We conclude that increasing obesity in the United States/Europe has probably not been fuelled by reduced physical activity leading to lowered TEE. We identify here a decline in adjusted BEE as a previously unrecognized factor.
|
|
