| 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. |
- 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.
|
|
| 4. |
- 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.
|
|
| 5. |
- 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.
|
|
| 6. |
- 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.
|
|
| 7. |
- 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.
|
|
| 8. |
- Keasar, Chen, et al.
(författare)
-
An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12
- 2018
-
Ingår i: Scientific Reports. - : NATURE PUBLISHING GROUP. - 2045-2322. ; 8
-
Tidskriftsartikel (refereegranskat)abstract
- Every two years groups worldwide participate in the Critical Assessment of Protein Structure Prediction (CASP) experiment to blindly test the strengths and weaknesses of their computational methods. CASP has significantly advanced the field but many hurdles still remain, which may require new ideas and collaborations. In 2012 a web-based effort called WeFold, was initiated to promote collaboration within the CASP community and attract researchers from other fields to contribute new ideas to CASP. Members of the WeFold coopetition (cooperation and competition) participated in CASP as individual teams, but also shared components of their methods to create hybrid pipelines and actively contributed to this effort. We assert that the scale and diversity of integrative prediction pipelines could not have been achieved by any individual lab or even by any collaboration among a few partners. The models contributed by the participating groups and generated by the pipelines are publicly available at the WeFold website providing a wealth of data that remains to be tapped. Here, we analyze the results of the 2014 and 2016 pipelines showing improvements according to the CASP assessment as well as areas that require further adjustments and research.
|
|
| 9. |
|
|
| 10. |
- Kosydar-Bochenek, J, et al.
(författare)
-
The Perception of the Patient Safety Climate by Health Professionals during the COVID-19 Pandemic-International Research
- 2022
-
Ingår i: International journal of environmental research and public health. - : MDPI AG. - 1660-4601. ; 19:15
-
Tidskriftsartikel (refereegranskat)abstract
- The patient safety climate is a key element of quality in healthcare. It should be a priority in the healthcare systems of all countries in the world. The goal of patient safety programs is to prevent errors and reduce the potential harm to patients when using healthcare services. A safety climate is also necessary to ensure a safe working environment for healthcare professionals. The attitudes of healthcare workers toward patient safety in various aspects of work, organization and functioning of the ward are important elements of the organization’s safety culture. The aim of this study was to determine the perception of the patient safety climate by healthcare workers during the COVID-19 pandemic. Methods: The study was conducted in five European countries. The Safety Attitude Questionnaire (SAQ) short version was used for the study. A total of 1061 healthcare workers: physicians, nurses and paramedics, participated in this study. Results: All groups received the highest mean results on the stress recognition subscale (SR): nurses 98.77, paramedics 96.39 and physician 98.28. Nurses and physicians evaluated work conditions (WC) to be the lowest (47.19 and 44.99), while paramedics evaluated perceptions of management (PM) as the worst (46.44). Paramedics achieved statistically significantly lower scores compared to nurses and physicians in job satisfaction (JS), stress recognition (SR) and perception of management (PM) (p < 0.0001). Paramedics compared to nurses and physicians rank better in working conditions (WC) in relation to patient safety (16.21%). Most often, persons of lower seniority scored higher in all subscales (p = 0.001). In Poland, Spain, France, Turkey, and Greece, healthcare workers scored highest in stress recognition (SR). In Poland, Spain, France, and Turkey, they assessed working conditions (WC) as the worst, while in Greece, the perception of management (PM) had the lowest result. Conclusion: Participant perceptions about the patient safety climate were not at a particularly satisfactory level, and there is still a need for the development of patient safety culture in healthcare in Europe. Overall, positive working conditions, good management and effective teamwork can contribute to improving employees’ attitudes toward patient safety. This study was carried out during the COVID-19 pandemic and should be repeated after its completion, and comparative studies will allow for a more precise determination of the safety climate in the assessment of employees.
|
|
