SwePub
Sök i SwePub databas

  Utökad sökning

Träfflista för sökning "WFRF:(Mathieu David) srt2:(2020-2024)"

Sökning: WFRF:(Mathieu David) > (2020-2024)

  • Resultat 1-50 av 67
Sortera/gruppera träfflistan
   
NumreringReferensOmslagsbildHitta
1.
  • Beal, Jacob, et al. (författare)
  • Robust estimation of bacterial cell count from optical density
  • 2020
  • Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
  • Tidskriftsartikel (refereegranskat)abstract
    • Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
  •  
2.
  • Abbasi, Rasha, et al. (författare)
  • IceCube search for neutrinos from GRB 221009A
  • 2023
  • Ingår i: Proceedings of 38th International Cosmic Ray Conference (ICRC 2023). - : Sissa Medialab Srl.
  • Konferensbidrag (refereegranskat)abstract
    •  GRB 221009A is the brightest Gamma Ray Burst (GRB) ever observed. The observed extremelyhigh flux of high and very-high-energy photons provide a unique opportunity to probe the predictedneutrino counterpart to the electromagnetic emission. We have used a variety of methods to searchfor neutrinos in coincidence with the GRB over several time windows during the precursor, promptand afterglow phases of the GRB. MeV scale neutrinos are studied using photo-multiplier ratescalers which are normally used to search for galactic core-collapse supernovae neutrinos. GeVneutrinos are searched starting with DeepCore triggers. These events don’t have directionallocalization, but instead can indicate an excess in the rate of events. 10 GeV - 1 TeV and >TeVneutrinos are searched using traditional neutrino point source methods which take into accountthe direction and time of events with DeepCore and the entire IceCube detector respectively. The>TeV results include both a fast-response analysis conducted by IceCube in real-time with timewindows of T0 − 1 to T0 + 2 hours and T0 ± 1 day around the time of GRB 221009A, as well asan offline analysis with 3 new time windows up to a time window of T0 − 1 to T0 + 14 days, thelongest time period we consider. The combination of observations by IceCube covers 9 ordersof magnitude in neutrino energy, from MeV to PeV, placing upper limits across the range forpredicted neutrino emission.
  •  
3.
  • Jin, Shoko, et al. (författare)
  • The wide-field, multiplexed, spectroscopic facility WEAVE : Survey design, overview, and simulated implementation
  • 2024
  • Ingår i: Monthly notices of the Royal Astronomical Society. - : Oxford University Press. - 0035-8711 .- 1365-2966. ; 530:3, s. 2688-2730
  • Tidskriftsartikel (refereegranskat)abstract
    • WEAVE, the new wide-field, massively multiplexed spectroscopic survey facility for the William Herschel Telescope, saw first light in late 2022. WEAVE comprises a new 2-deg field-of-view prime-focus corrector system, a nearly 1000-multiplex fibre positioner, 20 individually deployable 'mini' integral field units (IFUs), and a single large IFU. These fibre systems feed a dual-beam spectrograph covering the wavelength range 366-959nm at R similar to 5000, or two shorter ranges at . After summarizing the design and implementation of WEAVE and its data systems, we present the organization, science drivers, and design of a five- to seven-year programme of eight individual surveys to: (i) study our Galaxy's origins by completing Gaia's phase-space information, providing metallicities to its limiting magnitude for similar to 3 million stars and detailed abundances for similar to 1.5 million brighter field and open-cluster stars; (ii) survey similar to 0.4 million Galactic-plane OBA stars, young stellar objects, and nearby gas to understand the evolution of young stars and their environments; (iii) perform an extensive spectral survey of white dwarfs; (iv) survey similar to 400 neutral-hydrogen-selected galaxies with the IFUs; (v) study properties and kinematics of stellar populations and ionized gas in z < 0.5 cluster galaxies; (vi) survey stellar populations and kinematics in field galaxies at 0.3 less than or similar to z less than or similar to 0.7; (vii) study the cosmic evolution of accretion and star formation using >1 million spectra of LOFAR-selected radio sources; and (viii) trace structures using intergalactic/circumgalactic gas at z > 2. Finally, we describe the WEAVE Operational Rehearsals using the WEAVE Simulator.
  •  
4.
  • Thomas, Minta, et al. (författare)
  • Genome-wide Modeling of Polygenic Risk Score in Colorectal Cancer Risk.
  • 2020
  • Ingår i: American Journal of Human Genetics. - Cambridge : Elsevier BV. - 0002-9297 .- 1537-6605. ; 107:3, s. 432-444
  • Tidskriftsartikel (refereegranskat)abstract
    • Accurate colorectal cancer (CRC) risk prediction models are critical for identifying individuals at low and high risk of developing CRC, as they can then be offered targeted screening and interventions to address their risks of developing disease (if they are in a high-risk group) and avoid unnecessary screening and interventions (if they are in a low-risk group). As it is likely that thousands of genetic variants contribute to CRC risk, it is clinically important to investigate whether these genetic variants can be used jointly for CRC risk prediction. In this paper, we derived and compared different approaches to generating predictive polygenic risk scores (PRS) from genome-wide association studies (GWASs) including 55,105 CRC-affected case subjects and 65,079 control subjects of European ancestry. We built the PRS in three ways, using (1) 140 previously identified and validated CRC loci; (2) SNP selection based on linkage disequilibrium (LD) clumping followed by machine-learning approaches; and (3) LDpred, a Bayesian approach for genome-wide risk prediction. We tested the PRS in an independent cohort of 101,987 individuals with 1,699 CRC-affected case subjects. The discriminatory accuracy, calculated by the age- and sex-adjusted area under the receiver operating characteristics curve (AUC), was highest for the LDpred-derived PRS (AUC = 0.654) including nearly 1.2 M genetic variants (the proportion of causal genetic variants for CRC assumed to be 0.003), whereas the PRS of the 140 known variants identified from GWASs had the lowest AUC (AUC = 0.629). Based on the LDpred-derived PRS, we are able to identify 30% of individuals without a family history as having risk for CRC similar to those with a family history of CRC, whereas the PRS based on known GWAS variants identified only top 10% as having a similar relative risk. About 90% of these individuals have no family history and would have been considered average risk under current screening guidelines, but might benefit from earlier screening. The developed PRS offers a way for risk-stratified CRC screening and other targeted interventions.
  •  
5.
  • Thomas, Minta, et al. (författare)
  • Response to Li and Hopper
  • 2021
  • Ingår i: American Journal of Human Genetics. - : Elsevier BV. - 0002-9297 .- 1537-6605. ; 108:3, s. 527-529
  • Tidskriftsartikel (refereegranskat)
  •  
6.
  • Bousquet, Jean, et al. (författare)
  • ARIA digital anamorphosis : Digital transformation of health and care in airway diseases from research to practice
  • 2021
  • Ingår i: Allergy. European Journal of Allergy and Clinical Immunology. - : John Wiley & Sons. - 0105-4538 .- 1398-9995. ; 76:1, s. 168-190
  • Forskningsöversikt (refereegranskat)abstract
    • Digital anamorphosis is used to define a distorted image of health and care that may be viewed correctly using digital tools and strategies. MASK digital anamorphosis represents the process used by MASK to develop the digital transformation of health and care in rhinitis. It strengthens the ARIA change management strategy in the prevention and management of airway disease. The MASK strategy is based on validated digital tools. Using the MASK digital tool and the CARAT online enhanced clinical framework, solutions for practical steps of digital enhancement of care are proposed.
  •  
7.
  • Cuni-Sanchez, Aida, et al. (författare)
  • High aboveground carbon stock of African tropical montane forests
  • 2021
  • Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 596:7873, s. 536-542
  • Tidskriftsartikel (refereegranskat)abstract
    • Tropical forests store 40–50per cent of terrestrial vegetation carbon. However, spatial variations in aboveground live tree biomass carbon (AGC) stocks remain poorly understood, in particular in tropical montane forests. Owing to climatic and soil changes with increasing elevation, AGC stocks are lower in tropical montane forests compared with lowland forests. Here we assemble and analyse a dataset of structurally intact old-growth forests (AfriMont) spanning 44 montane sites in 12 African countries. We find that montane sites in the AfriMont plot network have a mean AGC stock of 149.4megagrams of carbon per hectare (95% confidence interval 137.1–164.2), which is comparable to lowland forests in the African Tropical Rainforest Observation Network4 and about 70per cent and 32per cent higher than averages from plot networks in montane and lowland forests in the Neotropics, respectively. Notably, our results are two-thirds higher than the Intergovernmental Panel on Climate Change default values for these forests in Africa8. We find that the low stem density and high abundance of large trees of African lowland forests is mirrored in the montane forests sampled. This carbon store is endangered: we estimate that 0.8 million hectares of old-growth African montane forest have been lost since 2000. We provide country-specific montane forest AGC stock estimates modelled from our plot network to helpto guide forest conservation and reforestation interventions. Our findings highlight the need for conserving these biodiverse and carbon-rich ecosystems.
  •  
8.
  • Lévy, Romain, et al. (författare)
  • Human CARMIL2 deficiency underlies a broader immunological and clinical phenotype than CD28 deficiency.
  • 2023
  • Ingår i: The Journal of experimental medicine. - : Rockefeller University Press. - 1540-9538 .- 0022-1007. ; 220:2
  • Tidskriftsartikel (refereegranskat)abstract
    • Patients with inherited CARMIL2 or CD28 deficiency have defective T cell CD28 signaling, but their immunological and clinical phenotypes remain largely unknown. We show that only one of three CARMIL2 isoforms is produced and functional across leukocyte subsets. Tested mutant CARMIL2 alleles from 89 patients and 52 families impair canonical NF-κB but not AP-1 and NFAT activation in T cells stimulated via CD28. Like CD28-deficient patients, CARMIL2-deficient patients display recalcitrant warts and low blood counts of CD4+ and CD8+ memory T cells and CD4+ TREGs. Unlike CD28-deficient patients, they have low counts of NK cells and memory B cells, and their antibody responses are weak. CARMIL2 deficiency is fully penetrant by the age of 10 yr and is characterized by numerous infections, EBV+ smooth muscle tumors, and mucocutaneous inflammation, including inflammatory bowel disease. Patients with somatic reversions of a mutant allele in CD4+ T cells have milder phenotypes. Our study suggests that CARMIL2 governs immunological pathways beyond CD28.
  •  
9.
  • Potapov, Anton M., et al. (författare)
  • Global fine-resolution data on springtail abundance and community structure
  • 2024
  • Ingår i: Scientific Data. - : Nature Publishing Group. - 2052-4463. ; 11:1
  • Tidskriftsartikel (refereegranskat)abstract
    • Springtails (Collembola) inhabit soils from the Arctic to the Antarctic and comprise an estimated ~32% of all terrestrial arthropods on Earth. Here, we present a global, spatially-explicit database on springtail communities that includes 249,912 occurrences from 44,999 samples and 2,990 sites. These data are mainly raw sample-level records at the species level collected predominantly from private archives of the authors that were quality-controlled and taxonomically-standardised. Despite covering all continents, most of the sample-level data come from the European continent (82.5% of all samples) and represent four habitats: woodlands (57.4%), grasslands (14.0%), agrosystems (13.7%) and scrublands (9.0%). We included sampling by soil layers, and across seasons and years, representing temporal and spatial within-site variation in springtail communities. We also provided data use and sharing guidelines and R code to facilitate the use of the database by other researchers. This data paper describes a static version of the database at the publication date, but the database will be further expanded to include underrepresented regions and linked with trait data.
  •  
10.
  • Abazajian, Kevork, et al. (författare)
  • CMB-S4 : Forecasting Constraints on Primordial Gravitational Waves
  • 2022
  • Ingår i: Astrophysical Journal. - : American Astronomical Society. - 0004-637X .- 1538-4357. ; 926:1
  • Tidskriftsartikel (refereegranskat)abstract
    • CMB-S4—the next-generation ground-based cosmic microwave background (CMB) experiment—is set to significantly advance the sensitivity of CMB measurements and enhance our understanding of the origin and evolution of the universe. Among the science cases pursued with CMB-S4, the quest for detecting primordial gravitational waves is a central driver of the experimental design. This work details the development of a forecasting framework that includes a power-spectrum-based semianalytic projection tool, targeted explicitly toward optimizing constraints on the tensor-to-scalar ratio, r, in the presence of Galactic foregrounds and gravitational lensing of the CMB. This framework is unique in its direct use of information from the achieved performance of current Stage 2–3 CMB experiments to robustly forecast the science reach of upcoming CMB-polarization endeavors. The methodology allows for rapid iteration over experimental configurations and offers a flexible way to optimize the design of future experiments, given a desired scientific goal. To form a closed-loop process, we couple this semianalytic tool with map-based validation studies, which allow for the injection of additional complexity and verification of our forecasts with several independent analysis methods. We document multiple rounds of forecasts for CMB-S4 using this process and the resulting establishment of the current reference design of the primordial gravitational-wave component of the Stage-4 experiment, optimized to achieve our science goals of detecting primordial gravitational waves for r > 0.003 at greater than 5σ, or in the absence of a detection, of reaching an upper limit of r < 0.001 at 95% CL.
  •  
11.
  • Ebrahimi-Fakhari, Darius, et al. (författare)
  • Defining the clinical, molecular and imaging spectrum of adaptor protein complex 4-associated hereditary spastic paraplegia
  • 2020
  • Ingår i: Brain. - OXFORD ENGLAND : Oxford University Press (OUP). - 0006-8950 .- 1460-2156. ; 143:10, s. 2929-2944
  • Tidskriftsartikel (refereegranskat)abstract
    • Bi-allelic loss-of-function variants in genes that encode subunits of the adaptor protein complex 4 (AP-4) lead to prototypical yet poorly understood forms of childhood-onset and complex hereditary spastic paraplegia: SPG47 (AP4B1), SPG50 (AP4M1), SPG51 (AP4E1) and SPG52 (AP4S1). Here, we report a detailed cross-sectional analysis of clinical, imaging and molecular data of 156 patients from 101 families. Enrolled patients were of diverse ethnic backgrounds and covered a wide age range (1.0-49.3 years). While the mean age at symptom onset was 0.8 +/- 0.6 years [standard deviation (SD), range 0.2-5.0], the mean age at diagnosis was 10.2 +/- 8.5 years (SD, range 0.1-46.3). We define a set of core features: early-onset developmental delay with delayed motor milestones and significant speech delay (50% non-verbal); intellectual disability in the moderate to severe range; mild hypotonia in infancy followed by spastic diplegia (mean age: 8.4 +/- 5.1 years, SD) and later tetraplegia (mean age: 16.1 +/- 9.8 years, SD); postnatal microcephaly (83%); foot deformities (69%); and epilepsy (66%) that is intractable in a subset. At last follow-up, 36% ambulated with assistance (mean age: 8.9 +/- 6.4 years, SD) and 54% were wheelchair-dependent (mean age: 13.4 +/- 9.8 years, SD). Episodes of stereotypic laughing, possibly consistent with a pseudobulbar affect, were found in 56% of patients. Key features on neuroimaging include a thin corpus callosum (90%), ventriculomegaly (65%) often with colpocephaly, and periventricular white-matter signal abnormalities (68%). Iron deposition and polymicrogyria were found in a subset of patients. AP4B1-associated SPG47 and AP4M1-associated SPG50 accounted for the majority of cases. About two-thirds of patients were born to consanguineous parents, and 82% carried homozygous variants. Over 70 unique variants were present, the majority of which are frameshift or nonsense mutations. To track disease progression across the age spectrum, we defined the relationship between disease severity as measured by several rating scales and disease duration. We found that the presence of epilepsy, which manifested before the age of 3 years in the majority of patients, was associated with worse motor outcomes. Exploring genotype-phenotype correlations, we found that disease severity and major phenotypes were equally distributed among the four subtypes, establishing that SPG47, SPG50, SPG51 and SPG52 share a common phenotype, an 'AP-4 deficiency syndrome'. By delineating the core clinical, imaging, and molecular features of AP-4-associated hereditary spastic paraplegia across the age spectrum our results will facilitate early diagnosis, enable counselling and anticipatory guidance of affected families and help define endpoints for future interventional trials.
  •  
12.
  • Glas, Gerie J., et al. (författare)
  • Ventilation practices in burn patients-an international prospective observational cohort study
  • 2021
  • Ingår i: BURNS & TRAUMA. - : Oxford University Press. - 2321-3868 .- 2321-3876. ; 9
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: It is unknown whether lung-protective ventilation is applied in burn patients and whether they benefit from it. This study aimed to determine ventilation practices in burn intensive care units (ICUs) and investigate the association between lung-protective ventilation and the number of ventilator-free days and alive at day 28 (VFD-28). Methods: This is an international prospective observational cohort study including adult burn patients requiring mechanical ventilation. Low tidal volume (V-T) was defined as V-T <= 8 mL/kg predicted body weight (PBW). Levels of positive end-expiratory pressure (PEEP) and maximum airway pressures were collected. The association between V-T and VFD-28 was analyzed using a competing risk model. Ventilation settings were presented for all patients, focusing on the first day of ventilation. We also compared ventilation settings between patients with and without inhalation trauma. Results: A total of 160 patients from 28 ICUs in 16 countries were included. Low V-T was used in 74% of patients, median V-T size was 7.3 [interquartile range (IQR) 6.2-8.3] mL/kg PBW and did not differ between patients with and without inhalation trauma (p= 0.58). Median VFD-28 was 17 (IQR 0-26), without a difference between ventilation with low or high V-T (p= 0.98). All patients were ventilated with PEEP levels >= 5 cmH(2)O; 80% of patients had maximum airway pressures <30 cmH(2)O. Conclusion: In this international cohort study we found that lung-protective ventilation is used in the majority of burn patients, irrespective of the presence of inhalation trauma. Use of low V-T was not associated with a reduction in VFD-28.
  •  
13.
  • Huijben, Jilske A, et al. (författare)
  • Changing care pathways and between-center practice variations in intensive care for traumatic brain injury across Europe : a CENTER-TBI analysis
  • 2020
  • Ingår i: Intensive Care Medicine. - : Springer Science and Business Media LLC. - 0342-4642 .- 1432-1238. ; 46:5, s. 995-1004
  • Tidskriftsartikel (refereegranskat)abstract
    • PURPOSE: To describe ICU stay, selected management aspects, and outcome of Intensive Care Unit (ICU) patients with traumatic brain injury (TBI) in Europe, and to quantify variation across centers.METHODS: This is a prospective observational multicenter study conducted across 18 countries in Europe and Israel. Admission characteristics, clinical data, and outcome were described at patient- and center levels. Between-center variation in the total ICU population was quantified with the median odds ratio (MOR), with correction for case-mix and random variation between centers.RESULTS: A total of 2138 patients were admitted to the ICU, with median age of 49 years; 36% of which were mild TBI (Glasgow Coma Scale; GCS 13-15). Within, 72 h 636 (30%) were discharged and 128 (6%) died. Early deaths and long-stay patients (> 72 h) had more severe injuries based on the GCS and neuroimaging characteristics, compared with short-stay patients. Long-stay patients received more monitoring and were treated at higher intensity, and experienced worse 6-month outcome compared to short-stay patients. Between-center variations were prominent in the proportion of short-stay patients (MOR = 2.3, p < 0.001), use of intracranial pressure (ICP) monitoring (MOR = 2.5, p < 0.001) and aggressive treatments (MOR = 2.9, p < 0.001); and smaller in 6-month outcome (MOR = 1.2, p = 0.01).CONCLUSIONS: Half of contemporary TBI patients at the ICU have mild to moderate head injury. Substantial between-center variations exist in ICU stay and treatment policies, and less so in outcome. It remains unclear whether admission of short-stay patients represents appropriate prudence or inappropriate use of clinical resources.
  •  
14.
  • Huijben, Jilske A., et al. (författare)
  • Use and impact of high intensity treatments in patients with traumatic brain injury across Europe : a CENTER-TBI analysis
  • 2021
  • Ingår i: Critical Care. - : BioMed Central (BMC). - 1364-8535 .- 1466-609X. ; 25:1
  • Tidskriftsartikel (refereegranskat)abstract
    • PURPOSE: To study variation in, and clinical impact of high Therapy Intensity Level (TIL) treatments for elevated intracranial pressure (ICP) in patients with traumatic brain injury (TBI) across European Intensive Care Units (ICUs).METHODS: We studied high TIL treatments (metabolic suppression, hypothermia (< 35 °C), intensive hyperventilation (PaCO2 < 4 kPa), and secondary decompressive craniectomy) in patients receiving ICP monitoring in the ICU stratum of the CENTER-TBI study. A random effect logistic regression model was used to determine between-centre variation in their use. A propensity score-matched model was used to study the impact on outcome (6-months Glasgow Outcome Score-extended (GOSE)), whilst adjusting for case-mix severity, signs of brain herniation on imaging, and ICP.RESULTS: 313 of 758 patients from 52 European centres (41%) received at least one high TIL treatment with significant variation between centres (median odds ratio = 2.26). Patients often transiently received high TIL therapies without escalation from lower tier treatments. 38% of patients with high TIL treatment had favourable outcomes (GOSE ≥ 5). The use of high TIL treatment was not significantly associated with worse outcome (285 matched pairs, OR 1.4, 95% CI [1.0-2.0]). However, a sensitivity analysis excluding high TIL treatments at day 1 or use of metabolic suppression at any day did reveal a statistically significant association with worse outcome.CONCLUSION: Substantial between-centre variation in use of high TIL treatments for TBI was found and treatment escalation to higher TIL treatments were often not preceded by more conventional lower TIL treatments. The significant association between high TIL treatments after day 1 and worse outcomes may reflect aggressive use or unmeasured confounders or inappropriate escalation strategies.TAKE HOME MESSAGE: Substantial variation was found in the use of highly intensive ICP-lowering treatments across European ICUs and a stepwise escalation strategy from lower to higher intensity level therapy is often lacking. Further research is necessary to study the impact of high therapy intensity treatments.TRIAL REGISTRATION: The core study was registered with ClinicalTrials.gov, number NCT02210221, registered 08/06/2014, https://clinicaltrials.gov/ct2/show/NCT02210221?id=NCT02210221&draw=1&rank=1 and with Resource Identification Portal (RRID: SCR_015582).
  •  
15.
  • Luo, Sizuo, et al. (författare)
  • Ultra-stable and versatile high-energy resolution setup for attosecond photoelectron spectroscopy
  • 2023
  • Ingår i: Advances in Physics: X. - 2374-6149. ; 8:1
  • Forskningsöversikt (refereegranskat)abstract
    • Attosecond photoelectron spectroscopy has opened up for studying light–matter interaction on ultrafast time scales. It is often performed with interferometric experimental setups that require outstanding stability. We demonstrate and characterize in detail an actively stabilized, versatile, high spectral resolution attosecond beamline based on a Mach-Zehnder interferometer. The active stabilization keeps the interferometer ultra-stable for several hours with an RMS stability of 13 as and a total pump-probe delay scanning range of (Formula presented.) fs. A tunable femtosecond laser source to drive high-order harmonic generation allows for precisely addressing atomic and molecular resonances. Furthermore, the interferometer includes a spectral shaper in 4f-geometry in the probe arm as well as a tunable bandpass filter in the pump arm, which offer additional high flexibility in terms of tunability as well as narrowband or polychromatic probe pulses. We demonstrate the capabilities of the beamline via experiments using several variants of the RABBIT (reconstruction of attosecond beating by two photon transitions) technique. In this setup, the temporal-spectral resolution of photoelectron spectroscopy can reach a new level of accuracy and precision.
  •  
16.
  • Sharrack, Basil, et al. (författare)
  • Autologous haematopoietic stem cell transplantation and other cellular therapy in multiple sclerosis and immune-mediated neurological diseases : updated guidelines and recommendations from the EBMT Autoimmune Diseases Working Party (ADWP) and the Joint Accreditation Committee of EBMT and ISCT (JACIE)
  • 2020
  • Ingår i: Bone Marrow Transplantation. - : Springer Nature. - 0268-3369 .- 1476-5365. ; 55:2, s. 283-306
  • Tidskriftsartikel (refereegranskat)abstract
    • These updated EBMT guidelines review the clinical evidence, registry activity and mechanisms of action of haematopoietic stem cell transplantation (HSCT) in multiple sclerosis (MS) and other immune-mediated neurological diseases and provide recommendations for patient selection, transplant technique, follow-up and future development. The major focus is on autologous HSCT (aHSCT), used in MS for over two decades and currently the fastest growing indication for this treatment in Europe, with increasing evidence to support its use in highly active relapsing remitting MS failing to respond to disease modifying therapies. aHSCT may have a potential role in the treatment of the progressive forms of MS with a significant inflammatory component and other immune-mediated neurological diseases, including chronic inflammatory demyelinating polyneuropathy, neuromyelitis optica, myasthenia gravis and stiff person syndrome. Allogeneic HSCT should only be considered where potential risks are justified. Compared with other immunomodulatory treatments, HSCT is associated with greater short-term risks and requires close interspeciality collaboration between transplant physicians and neurologists with a special interest in these neurological conditions before, during and after treatment in accredited HSCT centres. Other experimental cell therapies are developmental for these diseases and patients should only be treated on clinical trials.
  •  
17.
  • Volovici, Victor, et al. (författare)
  • Comparative effectiveness of intracranial hypertension management guided by ventricular versus intraparenchymal pressure monitoring : a CENTER-TBI study
  • 2022
  • Ingår i: Acta Neurochirurgica. - : Springer. - 0001-6268 .- 0942-0940. ; 164:7, s. 1693-1705
  • Tidskriftsartikel (refereegranskat)abstract
    • OBJECTIVE: To compare outcomes between patients with primary external ventricular device (EVD)-driven treatment of intracranial hypertension and those with primary intraparenchymal monitor (IP)-driven treatment.METHODS: The CENTER-TBI study is a prospective, multicenter, longitudinal observational cohort study that enrolled patients of all TBI severities from 62 participating centers (mainly level I trauma centers) across Europe between 2015 and 2017. Functional outcome was assessed at 6 months and a year. We used multivariable adjusted instrumental variable (IV) analysis with "center" as instrument and logistic regression with covariate adjustment to determine the effect estimate of EVD on 6-month functional outcome.RESULTS: A total of 878 patients of all TBI severities with an indication for intracranial pressure (ICP) monitoring were included in the present study, of whom 739 (84%) patients had an IP monitor and 139 (16%) an EVD. Patients included were predominantly male (74% in the IP monitor and 76% in the EVD group), with a median age of 46 years in the IP group and 48 in the EVD group. Six-month GOS-E was similar between IP and EVD patients (adjusted odds ratio (aOR) and 95% confidence interval [CI] OR 0.74 and 95% CI [0.36-1.52], adjusted IV analysis). The length of intensive care unit stay was greater in the EVD group than in the IP group (adjusted rate ratio [95% CI] 1.70 [1.34-2.12], IV analysis). One hundred eighty-seven of the 739 patients in the IP group (25%) required an EVD due to refractory ICPs.CONCLUSION: We found no major differences in outcomes of patients with TBI when comparing EVD-guided and IP monitor-guided ICP management. In our cohort, a quarter of patients that initially received an IP monitor required an EVD later for ICP control. The prevalence of complications was higher in the EVD group.
  •  
18.
  • Wiegers, Eveline Janine Anna, et al. (författare)
  • Fluid balance and outcome in critically ill patients with traumatic brain injury (CENTER-TBI and OzENTER-TBI) : a prospective, multicentre, comparative effectiveness study
  • 2021
  • Ingår i: Lancet Neurology. - : Elsevier. - 1474-4422 .- 1474-4465. ; 20:8, s. 627-638
  • Tidskriftsartikel (refereegranskat)abstract
    • BACKGROUND: Fluid therapy-the administration of fluids to maintain adequate organ tissue perfusion and oxygenation-is essential in patients admitted to the intensive care unit (ICU) with traumatic brain injury. We aimed to quantify the variability in fluid management policies in patients with traumatic brain injury and to study the effect of this variability on patients' outcomes.METHODS: We did a prospective, multicentre, comparative effectiveness study of two observational cohorts: CENTER-TBI in Europe and OzENTER-TBI in Australia. Patients from 55 hospitals in 18 countries, aged 16 years or older with traumatic brain injury requiring a head CT, and admitted to the ICU were included in this analysis. We extracted data on demographics, injury, and clinical and treatment characteristics, and calculated the mean daily fluid balance (difference between fluid input and loss) and mean daily fluid input during ICU stay per patient. We analysed the association of fluid balance and input with ICU mortality and functional outcome at 6 months, measured by the Glasgow Outcome Scale Extended (GOSE). Patient-level analyses relied on adjustment for key characteristics per patient, whereas centre-level analyses used the centre as the instrumental variable.FINDINGS: 2125 patients enrolled in CENTER-TBI and OzENTER-TBI between Dec 19, 2014, and Dec 17, 2017, were eligible for inclusion in this analysis. The median age was 50 years (IQR 31 to 66) and 1566 (74%) of patients were male. The median of the mean daily fluid input ranged from 1·48 L (IQR 1·12 to 2·09) to 4·23 L (3·78 to 4·94) across centres. The median of the mean daily fluid balance ranged from -0·85 L (IQR -1·51 to -0·49) to 1·13 L (0·99 to 1·37) across centres. In patient-level analyses, a mean positive daily fluid balance was associated with higher ICU mortality (odds ratio [OR] 1·10 [95% CI 1·07 to 1·12] per 0·1 L increase) and worse functional outcome (1·04 [1·02 to 1·05] per 0·1 L increase); higher mean daily fluid input was also associated with higher ICU mortality (1·05 [1·03 to 1·06] per 0·1 L increase) and worse functional outcome (1·04 [1·03 to 1·04] per 1-point decrease of the GOSE per 0·1 L increase). Centre-level analyses showed similar associations of higher fluid balance with ICU mortality (OR 1·17 [95% CI 1·05 to 1·29]) and worse functional outcome (1·07 [1·02 to 1·13]), but higher fluid input was not associated with ICU mortality (OR 0·95 [0·90 to 1·00]) or worse functional outcome (1·01 [0·98 to 1·03]).INTERPRETATION: In critically ill patients with traumatic brain injury, there is significant variability in fluid management, with more positive fluid balances being associated with worse outcomes. These results, when added to previous evidence, suggest that aiming for neutral fluid balances, indicating a state of normovolaemia, contributes to improved outcome.
  •  
19.
  • Yang, Dazhi, et al. (författare)
  • Verification of deterministic solar forecasts
  • 2020
  • Ingår i: Solar Energy. - : PERGAMON-ELSEVIER SCIENCE LTD. - 0038-092X .- 1471-1257. ; 210, s. 20-37
  • Tidskriftsartikel (refereegranskat)abstract
    • The field of energy forecasting has attracted many researchers from different fields (e.g., meteorology, data sciences, mechanical or electrical engineering) over the last decade. Solar forecasting is a fast-growing sub-domain of energy forecasting. Despite several previous attempts, the methods and measures used for verification of deterministic (also known as single-valued or point) solar forecasts are still far from being standardized, making forecast analysis and comparison difficult. To analyze and compare solar forecasts, the well-established Murphy-Winkler framework for distribution-oriented forecast verification is recommended as a standard practice. This framework examines aspects of forecast quality, such as reliability, resolution, association, or discrimination, and analyzes the joint distribution of forecasts and observations, which contains all time-independent information relevant to verification. To verify forecasts, one can use any graphical display or mathematical/statistical measure to provide insights and summarize the aspects of forecast quality. The majority of graphical methods and accuracy measures known to solar forecasters are specific methods under this general framework. Additionally, measuring the overall skillfulness of forecasters is also of general interest. The use of the root mean square error (RMSE) skill score based on the optimal convex combination of climatology and persistence methods is highly recommended. By standardizing the accuracy measure and reference forecasting method, the RMSE skill score allows-with appropriate caveats-comparison of forecasts made using different models, across different locations and time periods.
  •  
20.
  • Zaidi, Syed H., et al. (författare)
  • Landscape of somatic single nucleotide variants and indels in colorectal cancer and impact on survival
  • 2020
  • Ingår i: Nature Communications. - : Nature Publishing Group. - 2041-1723. ; 11:1
  • Tidskriftsartikel (refereegranskat)abstract
    • Colorectal cancer (CRC) is a biologically heterogeneous disease. To characterize its mutational profile, we conduct targeted sequencing of 205 genes for 2,105 CRC cases with survival data. Our data shows several findings in addition to enhancing the existing knowledge of CRC. We identify PRKCI, SPZ1, MUTYH, MAP2K4, FETUB, and TGFBR2 as additional genes significantly mutated in CRC. We find that among hypermutated tumors, an increased mutation burden is associated with improved CRC-specific survival (HR=0.42, 95% CI: 0.21-0.82). Mutations in TP53 are associated with poorer CRC-specific survival, which is most pronounced in cases carrying TP53 mutations with predicted 0% transcriptional activity (HR=1.53, 95% CI: 1.21-1.94). Furthermore, we observe differences in mutational frequency of several genes and pathways by tumor location, stage, and sex. Overall, this large study provides deep insights into somatic mutations in CRC, and their potential relationships with survival and tumor features. Large scale sequencing study is of paramount importance to unravel the heterogeneity of colorectal cancer. Here, the authors sequenced 205 cancer genes in more than 2000 tumours and identified additional mutated driver genes, determined that mutational burden and specific mutations in TP53 are associated with survival odds.
  •  
21.
  •  
22.
  • Baxter, Amanda L., et al. (författare)
  • Collaborative experience between scientific software projects using Agile Scrum development
  • 2022
  • Ingår i: Software, practice & experience. - : John Wiley & Sons. - 0038-0644 .- 1097-024X. ; 52:10, s. 2077-2096
  • Tidskriftsartikel (refereegranskat)abstract
    • Developing sustainable software for the scientific community requires expertise in software engineering and domain science. This can be challenging due to the unique needs of scientific software, the insufficient resources for software engineering practices in the scientific community, and the complexity of developing for evolving scientific contexts. While open-source software can partially address these concerns, it can introduce complicating dependencies and delay development. These issues can be reduced if scientists and software developers collaborate. We present a case study wherein scientists from the SuperNova Early Warning System collaborated with software developers from the Scalable Cyberinfrastructure for Multi-Messenger Astrophysics project. The collaboration addressed the difficulties of open-source software development, but presented additional risks to each team. For the scientists, there was a concern of relying on external systems and lacking control in the development process. For the developers, there was a risk in supporting a user-group while maintaining core development. These issues were mitigated by creating a second Agile Scrum framework in parallel with the developers' ongoing Agile Scrum process. This Agile collaboration promoted communication, ensured that the scientists had an active role in development, and allowed the developers to evaluate and implement the scientists' software requirements. The collaboration provided benefits for each group: the scientists actuated their development by using an existing platform, and the developers utilized the scientists' use-case to improve their systems. This case study suggests that scientists and software developers can avoid scientific computing issues by collaborating and that Agile Scrum methods can address emergent concerns.
  •  
23.
  • Busto, David, et al. (författare)
  • Probing electronic decoherence with high-resolution attosecond photoelectron interferometry
  • 2022
  • Ingår i: European Physical Journal D. - : Springer Science and Business Media LLC. - 1434-6060 .- 1434-6079. ; 76:7
  • Tidskriftsartikel (refereegranskat)abstract
    • Abstract: Quantum coherence plays a fundamental role in the study and control of ultrafast dynamics in matter. In the case of photoionization, entanglement of the photoelectron with the ion is a well-known source of decoherence when only one of the particles is measured. Here, we investigate decoherence due to entanglement of the radial and angular degrees of freedom of the photoelectron. We study two-photon ionization via the 2s2p autoionizing state in He using high spectral resolution photoelectron interferometry. Combining experiment and theory, we show that the strong dipole coupling of the 2s2p and 2p2 states results in the entanglement of the angular and radial degrees of freedom. This translates, in angle-integrated measurements, into a dynamic loss of coherence during autoionization. Graphic Abstract: [Figure not available: see fulltext.]. © 2022, The Author(s).
  •  
24.
  • Charpin, Laurent, et al. (författare)
  • Ageing and air leakage assessment of a nuclear reactor containment mock-up : VERCORS 2nd benchmark
  • 2021
  • Ingår i: Nuclear Engineering and Design. - : Elsevier BV. - 0029-5493. ; 377
  • Tidskriftsartikel (refereegranskat)abstract
    • Electricité de France (EDF) operates a large fleet of nuclear reactors and is responsible for demonstrating the safety of facilities, including concrete containment buildings (CCB), which are non-replaceable components. The leak-tightness of CCBs is assessed every 10 years during integrated leak-rate tests (IRLT). For double-wall containments, which have no metallic liners, the leak-tightness is strongly influenced by the degree of cracking of concrete and opening of the cracks, which mostly depends on (a) the prestress decrease due to the delayed strains of concrete and to a lesser extent due to relaxation of tendons steel, and (b) the saturation degree of the Powered by Editorial Manager® and ProduXion Manager® from Aries Systems Corporation concrete wall. Therefore, to optimize the maintenance programs on CCBs, it is important to predict the evolution of drying, creep and shrinkage strains of concrete to be able to correctly assess the pre-stress losses, and finally the air leak-tightness at a structural level during pressure tests or under accidental loadings. To improve our understanding and identify the best modelling practices on this issue, a large experimental program called VERCORS was launched in 2014. VERCORS is a 1/3 mock-up of a 1300 MWe nuclear reactor CCB. It has been widely instrumented, and its concrete thoroughly characterized. A specific attention has been paid to ensure it is consistent with real CBBs features in EDF's nuclear fleet. To complement its internal R&D efforts, EDF decided to associate external partners to this program. One of the means for this is the organization of benchmarks, where all teams are given data and information about the mock-up and are asked to quantitatively predict its behaviour. The present paper reports the organization and findings of the 2nd benchmark which was organized in 2018 and gathered several international teams around the same objective: improve the confidence in the modelling of structural behaviour as well as the leak-tightness of concrete in containment walls under pressure test loading. The benchmark has shown once again that predicting the mechanical and leakage behaviour of containment buildings is a difficult task. The benchmark also yielded interesting information about the possibility to use spatially reduced models to predict the mechanical behaviour and leakage and underlined the fact that more research must be done to better predict the localization of cracks and leakage. Some lessons have been learnt for the next benchmark: EDF will ask to clarify further the calibration methods, will give more data (including drying, creep and shrinkage at different temperatures and moisture measurements in the mock-up), and will help the participants using local leakage data by projecting the raw measurements on a regular grid, so that the local leakage models can be improved.
  •  
25.
  • Cheraghi, Saeid, et al. (författare)
  • Seismic imaging across fault systems in the Abitibi greenstone belt : an analysis of pre- and post-stack migration approaches in the Chibougamau area, Quebec, Canada
  • 2021
  • Ingår i: Solid Earth. - : Copernicus Publications. - 1869-9510 .- 1869-9529. ; 12:5, s. 1143-1164
  • Tidskriftsartikel (refereegranskat)abstract
    • Two high-resolution seismic reflection profiles acquired north and south of Chibougamau, located in the northeast of the Abitibi subprovince of Canada, help understand historic volcanically hosted massive sulfide (VMS) deposits and hydrothermal Cu-Au mineralization found there. Major faults crossed by the profiles include the Barlow fault in the north and the Doda fault and the Guercheville fault in the south, all targets of this study that seeks to determine spatial relationships with a known metal endowment in the area. Common-offset DMO corrections and common-offset pre-stack time migrations (PSTMs) were considered. Irregularities of the trace midpoint distribution resulting from the crooked geometry of both profiles and their relative contribution to the DMO and PSTM methods and seismic illumination were assessed in the context of the complex subsurface architecture of the area. To scrutinize this contribution, seismic images were generated for offset ranges of 0-9 km using increments of 3 km. Migration of out-of-plane reflections used cross-dip element analysis to accurately estimate the fault dip. The seismic imaging shows the thickening of the upper-crustal rocks near the fault zones along both profiles. In the northern seismic reflection section, the key geological structures identified include the Barlow fault and two diffraction sets imaged within the fault zone that represent potential targets for future exploration. The south seismic reflection section shows rather a complicated geometry of two fault systems. The Guercheville fault observed as a subhorizontal reflector connects to a steeply dipping reflector. The Doda fault dips subvertical in the shallow crust but as a steeply dipping reflection set at depth. Nearby gold showings suggest that these faults may help channel and concentrate mineralizing fluids.
  •  
26.
  • Cooper, Thomas M., et al. (författare)
  • Nanoscale Organization of a Platinum(II) Acetylide Cholesteric Liquid Crystal Molecular Glass for Photonics Applications
  • 2020
  • Ingår i: Advanced Functional Materials. - : Wiley. - 1616-301X .- 1616-3028. ; 30:28
  • Tidskriftsartikel (refereegranskat)abstract
    • The fabrication, molecular structure, and spectroscopy of a stable cholesteric liquid crystal platinum acetylide glass obtained from trans-Pt(PEt3)(2)(C(sic)C-C6H5-C(sic)N)(C(sic)C-C6H5-COO-Cholesterol), are described and designated as PE1-CN-Chol. Polarized optical microscopy, differential scanning calorimetry, and wide-angle X-ray scattering experiments show room temperature glassy/crystalline texture with crystal formation upon heating to 165 degrees C. Further heating results in conversion to cholesteric phase. Cooling to room temperature leads to the formation of a cholesteric liquid crystal glass. Scanning tunneling microscopy of a PE1-CN-Chol monolayer reveals self-assembly at the solid-liquid interface with an array of two molecules arranged in pairs, oriented head-to-head through the CN groups, giving rise to a lamella arrangement. The lamella structure obtained from molecular dynamics calculations shows a clear phase separation between the conjugated platinum acetylide and the hydrophobic cholesterol moiety with the lamellae separation distance being 4.0 nm. Ultrafast transient absorption and flash photolysis spectra of the glass show intersystem crossing to the triplet state occurring within 100 ps following excitation. The triplet decay time of the film compared to aerated and deoxygenated solutions is consistent with oxygen quenching at the film surface but not within the film. The high chromophore concentration, high glass thermal stability, and long triplet lifetime in air show that these materials have potential as nonlinear absorbing materials.
  •  
27.
  • Dijkland, Simone A., et al. (författare)
  • Outcome Prediction after Moderate and Severe Traumatic Brain Injury : External Validation of Two Established Prognostic Models in 1742 European Patients
  • 2021
  • Ingår i: Journal of Neurotrauma. - : Mary Ann Liebert. - 0897-7151 .- 1557-9042. ; 38:10, s. 1377-1388
  • Tidskriftsartikel (refereegranskat)abstract
    • The International Mission on Prognosis and Analysis of Clinical Trials in Traumatic Brain Injury (IMPACT) and Corticoid Randomisation After Significant Head injury (CRASH) prognostic models predict functional outcome after moderate and severe traumatic brain injury (TBI). We aimed to assess their performance in a contemporary cohort of patients across Europe. The Collaborative European NeuroTrauma Effectiveness Research in Traumatic Brain Injury (CENTER-TBI) core study is a prospective, observational cohort study in patients presenting with TBI and an indication for brain computed tomography. The CENTER-TBI core cohort consists of 4509 TBI patients available for analyses from 59 centers in 18 countries across Europe and Israel. The IMPACT validation cohort included 1173 patients with GCS ≤12, age ≥14, and 6-month Glasgow Outcome Scale-Extended (GOSE) available. The CRASH validation cohort contained 1742 patients with GCS ≤14, age ≥16, and 14-day mortality or 6-month GOSE available. Performance of the three IMPACT and two CRASH model variants was assessed with discrimination (area under the receiver operating characteristic curve; AUC) and calibration (comparison of observed vs. predicted outcome rates). For IMPACT, model discrimination was good, with AUCs ranging between 0.77 and 0.85 in 1173 patients and between 0.80 and 0.88 in the broader CRASH selection (n = 1742). For CRASH, AUCs ranged between 0.82 and 0.88 in 1742 patients and between 0.66 and 0.80 in the stricter IMPACT selection (n = 1173). Calibration of the IMPACT and CRASH models was generally moderate, with calibration-in-the-large and calibration slopes ranging between -2.02 and 0.61 and between 0.48 and 1.39, respectively. The IMPACT and CRASH models adequately identify patients at high risk for mortality or unfavorable outcome, which supports their use in research settings and for benchmarking in the context of quality-of-care assessment.
  •  
28.
  • Ducharme, Simon, et al. (författare)
  • Recommendations to distinguish behavioural variant frontotemporal dementia from psychiatric disorders
  • 2020
  • Ingår i: Brain. - : Oxford University Press (OUP). - 0006-8950 .- 1460-2156. ; 143:6, s. 1632-1650
  • Tidskriftsartikel (refereegranskat)abstract
    • The behavioural variant of frontotemporal dementia (bvFTD) is a frequent cause of early-onset dementia. The diagnosis of bvFTD remains challenging because of the limited accuracy of neuroimaging in the early disease stages and the absence of molecular biomarkers, and therefore relies predominantly on clinical assessment. BvFTD shows significant symptomatic overlap with non-degenerative primary psychiatric disorders including major depressive disorder, bipolar disorder, schizophrenia, obsessive-compulsive disorder, autism spectrum disorders and even personality disorders. To date, ∼50% of patients with bvFTD receive a prior psychiatric diagnosis, and average diagnostic delay is up to 5-6 years from symptom onset. It is also not uncommon for patients with primary psychiatric disorders to be wrongly diagnosed with bvFTD. The Neuropsychiatric International Consortium for Frontotemporal Dementia was recently established to determine the current best clinical practice and set up an international collaboration to share a common dataset for future research. The goal of the present paper was to review the existing literature on the diagnosis of bvFTD and its differential diagnosis with primary psychiatric disorders to provide consensus recommendations on the clinical assessment. A systematic literature search with a narrative review was performed to determine all bvFTD-related diagnostic evidence for the following topics: bvFTD history taking, psychiatric assessment, clinical scales, physical and neurological examination, bedside cognitive tests, neuropsychological assessment, social cognition, structural neuroimaging, functional neuroimaging, CSF and genetic testing. For each topic, responsible team members proposed a set of minimal requirements, optimal clinical recommendations, and tools requiring further research or those that should be developed. Recommendations were listed if they reached a ≥ 85% expert consensus based on an online survey among all consortium participants. New recommendations include performing at least one formal social cognition test in the standard neuropsychological battery for bvFTD. We emphasize the importance of 3D-T1 brain MRI with a standardized review protocol including validated visual atrophy rating scales, and to consider volumetric analyses if available. We clarify the role of 18F-fluorodeoxyglucose PET for the exclusion of bvFTD when normal, whereas non-specific regional metabolism abnormalities should not be over-interpreted in the case of a psychiatric differential diagnosis. We highlight the potential role of serum or CSF neurofilament light chain to differentiate bvFTD from primary psychiatric disorders. Finally, based on the increasing literature and clinical experience, the consortium determined that screening for C9orf72 mutation should be performed in all possible/probable bvFTD cases or suspected cases with strong psychiatric features.
  •  
29.
  • Etzold, Sophia, et al. (författare)
  • Nitrogen deposition is the most important environmental driver of growth of pure, even-aged and managed European forests
  • 2020
  • Ingår i: Forest Ecology and Management. - : Elsevier BV. - 0378-1127 .- 1872-7042. ; 458
  • Tidskriftsartikel (refereegranskat)abstract
    • Changing environmental conditions may substantially interact with site quality and forest stand characteristics, and impact forest growth and carbon sequestration. Understanding the impact of the various drivers of forest growth is therefore critical to predict how forest ecosystems can respond to climate change. We conducted a continental-scale analysis of recent (1995–2010) forest volume increment data (ΔVol, m3 ha−1 yr−1), obtained from ca. 100,000 coniferous and broadleaved trees in 442 even-aged, single-species stands across 23 European countries. We used multivariate statistical approaches, such as mixed effects models and structural equation modelling to investigate how European forest growth respond to changes in 11 predictors, including stand characteristics, climate conditions, air and site quality, as well as their interactions. We found that, despite the large environmental gradients encompassed by the forests examined, stand density and age were key drivers of forest growth. We further detected a positive, in some cases non-linear effect of N deposition, most pronounced for beech forests, with a tipping point at ca. 30 kg N ha−1 yr−1. With the exception of a consistent temperature signal on Norway spruce, climate-related predictors and ground-level ozone showed much less generalized relationships with ΔVol. Our results show that, together with the driving forces exerted by stand density and age, N deposition is at least as important as climate to modulate forest growth at continental scale in Europe, with a potential negative effect at sites with high N deposition.
  •  
30.
  • Fehlinger, Lena, et al. (författare)
  • The ecological role of permanent ponds in Europe : a review of dietary linkages to terrestrial ecosystems via emerging insects
  • 2023
  • Ingår i: Inland Waters. - : Taylor & Francis. - 2044-2041 .- 2044-205X. ; 13:1, s. 30-46
  • Forskningsöversikt (refereegranskat)abstract
    • Permanent ponds are valuable freshwater systems and biodiversity hotspots. They provide diverse ecosystem services (ESs), including water quality improvement and supply, food provisioning, and biodiversity support, despite significant pressure from multiple anthropogenic stressors and the impacts of ongoing global change. However, ponds are largely overlooked in management plans and legislation, and ecological research has focused on large freshwater ecosystems, such as rivers or lakes. Protection of ponds is often insufficient or indirectly provided via associated habitats such as wetlands. This situation is likely exacerbated by the lack of a full-scale understanding of the importance of ponds. In this review, we provide a detailed overview of permanent ponds across Europe, including their usages and the biodiversity they support. By discussing the concepts of pondscape and metacommunity theory, we highlight the importance of connectivity among and between ponds and identified fluxes of emerging insects as another ES of ponds. Those insects are rich in essential nutrients such as polyunsaturated fatty acids (PUFAs), delivered through them to the terrestrial environment; however, the extent and impact of this ES remains largely unexplored. Several potential stressors, especially related to ongoing global change, that influence pond diversity and integrity are discussed. We provide our insights on future pond management. Adaptive measures, taking into account the pond system per se within the pondscape, are the most promising to mitigate the loss of natural ponds and restore and conserve natural small waterbodies as refuges and diversity hotspots in increasingly urbanized landscapes.
  •  
31.
  • Gainar, Adrian, et al. (författare)
  • Tuning the Organogelating and Spectroscopic Properties of a C-3-Symmetric Pyrene-Based Gelator through Charge Transfer
  • 2021
  • Ingår i: Chemistry - A European Journal. - : WILEY-V C H VERLAG GMBH. - 0947-6539 .- 1521-3765. ; 27:7, s. 2410-2420
  • Tidskriftsartikel (refereegranskat)abstract
    • Two-component organogels and xerogels based on a C-3-symmetric pyrene-containing gelator have been deeply characterized through a wide range of techniques. Based on the formation of charge transfer complexes, the gelation phenomenon proved to be highly dependent on the nature of the electron poor dopant. This parameter significantly influenced the corresponding gelation domains, the critical gelation concentrations of acceptor dopants, the gel-to-sol transition temperatures, the microstructures formed in the xerogel state and their spectroscopic properties. In particular, titrations and variable-temperature UV-visible absorption spectroscopy demonstrated the key role of donor-acceptor interactions with a remarkable correlation between the phase transition temperatures and the disappearance of the characteristic charge transfer bands. The assignment of these electronic transitions was confirmed through time-dependent density functional theory (TD-DFT) calculations. Eventually, it was shown that the luminescent properties of these materials can be tuned with the temperature, either in intensity or emission wavelength.
  •  
32.
  • Gonzalez-Sanchez, Marina, et al. (författare)
  • Stacked or Folded? : Impact of Chelate Cooperativity on the Self-Assembly Pathway to Helical Nanotubes from Dinucleobase Monomers
  • 2023
  • Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 145:32, s. 17805-17818
  • Tidskriftsartikel (refereegranskat)abstract
    • Self-assembled nanotubesexhibit impressive biologicalfunctionsthat have always inspired supramolecular scientists in their effortsto develop strategies to build such structures from small moleculesthrough a bottom-up approach. One of these strategies employs moleculesendowed with self-recognizing motifs at the edges, which can undergoeither cyclization-stacking or folding-polymerizationprocesses that lead to tubular architectures. Which of these self-assemblypathways is ultimately selected by these molecules is, however, oftendifficult to predict and even to evaluate experimentally. We showhere a unique example of two structurally related molecules substitutedwith complementary nucleobases at the edges (i.e., G:C and A:U) for which the supramolecular pathway takenis determined by chelate cooperativity, that is, by their propensityto assemble in specific cyclic structures through Watson-Crickpairing. Because of chelate cooperativities that differ in severalorders of magnitude, these molecules exhibit distinct supramolecularscenarios prior to their polymerization that generate self-assemblednanotubes with different internal monomer arrangements, either stackedor coiled, which lead at the same time to opposite helicities andchiroptical properties.
  •  
33.
  • Grünig, Marc, et al. (författare)
  • A harmonized database of European forest simulations under climate change
  • 2024
  • Ingår i: Data in Brief. - 2352-3409. ; 54
  • Tidskriftsartikel (refereegranskat)abstract
    • Process-based forest models combine biological, physical, and chemical process understanding to simulate forest dynamics as an emergent property of the system. As such, they are valuable tools to investigate the effects of climate change on forest ecosystems. Specifically, they allow testing of hypotheses regarding long-term ecosystem dynamics and provide means to assess the impacts of climate scenarios on future forest development. As a consequence, numerous local-scale simulation studies have been conducted over the past decades to assess the impacts of climate change on forests. These studies apply the best available models tailored to local conditions, parameterized and evaluated by local experts. However, this treasure trove of knowledge on climate change responses remains underexplored to date, as a consistent and harmonized dataset of local model simulations is missing. Here, our objectives were (i) to compile existing local simulations on forest development under climate change in Europe in a common database, (ii) to harmonize them to a common suite of output variables, and (iii) to provide a standardized vector of auxiliary environmental variables for each simulated location to aid subsequent investigations. Our dataset of European stand- and landscape-level forest simulations contains over 1.1 million simulation runs representing 135 million simulation years for more than 13,000 unique locations spread across Europe. The data were harmonized to consistently describe forest development in terms of stand structure (dominant height), composition (dominant species, admixed species), and functioning (leaf area index). Auxiliary variables provided include consistent daily climate information (temperature, precipitation, radiation, vapor pressure deficit) as well as information on local site conditions (soil depth, soil physical properties, soil water holding capacity, plant-available nitrogen). The present dataset facilitates analyses across models and locations, with the aim to better harness the valuable information contained in local simulations for large-scale policy support, and for fostering a deeper understanding of the effects of climate change on forest ecosystems in Europe.
  •  
34.
  • Huijben, Jilske A, et al. (författare)
  • Quality indicators for patients with traumatic brain injury in European intensive care units : a CENTER-TBI study.
  • 2020
  • Ingår i: Critical Care. - : Springer Science and Business Media LLC. - 1364-8535 .- 1466-609X. ; 24:1
  • Tidskriftsartikel (refereegranskat)abstract
    • BACKGROUND: The aim of this study is to validate a previously published consensus-based quality indicator set for the management of patients with traumatic brain injury (TBI) at intensive care units (ICUs) in Europe and to study its potential for quality measurement and improvement.METHODS: Our analysis was based on 2006 adult patients admitted to 54 ICUs between 2014 and 2018, enrolled in the CENTER-TBI study. Indicator scores were calculated as percentage adherence for structure and process indicators and as event rates or median scores for outcome indicators. Feasibility was quantified by the completeness of the variables. Discriminability was determined by the between-centre variation, estimated with a random effect regression model adjusted for case-mix severity and quantified by the median odds ratio (MOR). Statistical uncertainty of outcome indicators was determined by the median number of events per centre, using a cut-off of 10.RESULTS: A total of 26/42 indicators could be calculated from the CENTER-TBI database. Most quality indicators proved feasible to obtain with more than 70% completeness. Sub-optimal adherence was found for most quality indicators, ranging from 26 to 93% and 20 to 99% for structure and process indicators. Significant (p < 0.001) between-centre variation was found in seven process and five outcome indicators with MORs ranging from 1.51 to 4.14. Statistical uncertainty of outcome indicators was generally high; five out of seven had less than 10 events per centre.CONCLUSIONS: Overall, nine structures, five processes, but none of the outcome indicators showed potential for quality improvement purposes for TBI patients in the ICU. Future research should focus on implementation efforts and continuous reevaluation of quality indicators.TRIAL REGISTRATION: The core study was registered with ClinicalTrials.gov, number NCT02210221, registered on August 06, 2014, with Resource Identification Portal (RRID: SCR_015582).
  •  
35.
  • Jakobsson, Martin, et al. (författare)
  • The International Bathymetric Chart of the Arctic Ocean Version 4.0
  • 2020
  • Ingår i: Scientific Data. - : Springer Science and Business Media LLC. - 2052-4463. ; 7:1
  • Tidskriftsartikel (refereegranskat)abstract
    • Bathymetry (seafloor depth), is a critical parameter providing the geospatial context for a multitude of marine scientific studies. Since 1997, the International Bathymetric Chart of the Arctic Ocean (IBCAO) has been the authoritative source of bathymetry for the Arctic Ocean. IBCAO has merged its efforts with the Nippon Foundation-GEBCO-Seabed 2030 Project, with the goal of mapping all of the oceans by 2030. Here we present the latest version (IBCAO Ver. 4.0), with more than twice the resolution (200 x 200m versus 500 x 500m) and with individual depth soundings constraining three times more area of the Arctic Ocean (similar to 19.8% versus 6.7%), than the previous IBCAO Ver. 3.0 released in 2012. Modern multibeam bathymetry comprises similar to 14.3% in Ver. 4.0 compared to similar to 5.4% in Ver. 3.0. Thus, the new IBCAO Ver. 4.0 has substantially more seafloor morphological information that offers new insights into a range of submarine features and processes; for example, the improved portrayal of Greenland fjords better serves predictive modelling of the fate of the Greenland Ice Sheet. Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.12369314
  •  
36.
  • Khankari, Nikhil K, et al. (författare)
  • Mendelian Randomization of Circulating Polyunsaturated Fatty Acids and Colorectal Cancer Risk.
  • 2020
  • Ingår i: Cancer Epidemiology, Biomarkers and Prevention. - 1055-9965 .- 1538-7755. ; 29:4, s. 860-870
  • Tidskriftsartikel (refereegranskat)abstract
    • BACKGROUND: Results from epidemiologic studies examining polyunsaturated fatty acids (PUFA) and colorectal cancer risk are inconsistent. Mendelian randomization may strengthen causal inference from observational studies. Given their shared metabolic pathway, examining the combined effects of aspirin/NSAID use with PUFAs could help elucidate an association between PUFAs and colorectal cancer risk.METHODS: Information was leveraged from genome-wide association studies (GWAS) regarding PUFA-associated SNPs to create weighted genetic scores (wGS) representing genetically predicted circulating blood PUFAs for 11,016 non-Hispanic white colorectal cancer cases and 13,732 controls in the Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO). Associations per SD increase in the wGS were estimated using unconditional logistic regression. Interactions between PUFA wGSs and aspirin/NSAID use on colorectal cancer risk were also examined.RESULTS: Modest colorectal cancer risk reductions were observed per SD increase in circulating linoleic acid [ORLA = 0.96; 95% confidence interval (CI) = 0.93-0.98; P = 5.2 × 10-4] and α-linolenic acid (ORALA = 0.95; 95% CI = 0.92-0.97; P = 5.4 × 10-5), whereas modest increased risks were observed for arachidonic (ORAA = 1.06; 95% CI = 1.03-1.08; P = 3.3 × 10-5), eicosapentaenoic (OREPA = 1.04; 95% CI = 1.01-1.07; P = 2.5 × 10-3), and docosapentaenoic acids (ORDPA = 1.03; 95% CI = 1.01-1.06; P = 1.2 × 10-2). Each of these effects was stronger among aspirin/NSAID nonusers in the stratified analyses.CONCLUSIONS: Our study suggests that higher circulating shorter-chain PUFAs (i.e., LA and ALA) were associated with reduced colorectal cancer risk, whereas longer-chain PUFAs (i.e., AA, EPA, and DPA) were associated with an increased colorectal cancer risk.IMPACT: The interaction of PUFAs with aspirin/NSAID use indicates a shared colorectal cancer inflammatory pathway. Future research should continue to improve PUFA genetic instruments to elucidate the independent effects of PUFAs on colorectal cancer.
  •  
37.
  • Marszalek, Jaroslaw, et al. (författare)
  • J-domain proteins : From molecular mechanisms to diseases
  • 2024
  • Ingår i: Cell stress & chaperones (Print). - 1355-8145 .- 1466-1268. ; 29:1, s. 21-33
  • Tidskriftsartikel (refereegranskat)abstract
    • J-domain proteins (JDPs) are the largest family of chaperones in most organisms, but much of how they function within the network of other chaperones and protein quality control machineries is still an enigma. Here, we report on the latest findings related to JDP functions presented at a dedicated JDP workshop in Gdansk, Poland. The report does not include all (details) of what was shared and discussed at the meeting, because some of these original data have not yet been accepted for publication elsewhere or represented still preliminary observations at the time.
  •  
38.
  •  
39.
  •  
40.
  • Mathieu, David, et al. (författare)
  • The Data Loop : how audiences and media actors make datafication work
  • 2020
  • Ingår i: MedieKultur. - : SMID. - 0900-9671 .- 1901-9726. ; :69, s. 116-138
  • Tidskriftsartikel (refereegranskat)abstract
    • As our digital footprints are collected and analysed by the media and fed back at us as new experiences, providing more data to collect, data circulates in a loop from audiences to media and back. This data loop is for media studies an occasion to revisit the media–audience nexus in an age of datafication. We argue that an audience perspective is needed in order to break with the structure–agency linearity in the current understanding of datafication. In this article, we develop a model of the data loop that first presents the fundamentals of data circulation between social actors and digital interfaces, then the moments of agency between actors in a relation of mutual dependence. The article closes with a discussion of previous models within media and communication that have addressed similar ideas, such as audience feedback, mutuality and circularity.
  •  
41.
  • Mathieu, François, et al. (författare)
  • Impact of Antithrombotic Agents on Radiological Lesion Progression in Acute Traumatic Brain Injury : A CENTER-TBI Propensity-Matched Cohort Analysis
  • 2020
  • Ingår i: Journal of Neurotrauma. - : Mary Ann Liebert. - 0897-7151 .- 1557-9042. ; 37:19, s. 2069-2080
  • Tidskriftsartikel (refereegranskat)abstract
    • An increasing number of elderly patients are being affected by traumatic brain injury (TBI) and a significant proportion are on pre-hospital antithrombotic therapy for cardio- or cerebrovascular indications. We have quantified the impact of antiplatelet/anticoagulant (APAC) agents on radiological lesion progression in acute TBI, using a novel, semi-automated approach to volumetric lesion measurement, and explored the impact of use on clinical outcomes in the Collaborative European NeuroTrauma Effectiveness Research in Traumatic Brain Injury (CENTER-TBI) study. We used a 1:1 propensity-matched cohort design, matching controls to APAC users based on demographics, baseline clinical status, pre-injury comorbidities, and injury severity. Subjects were selected from a pool of patients enrolled in CENTER-TBI with computed tomography (CT) scan at admission and repeated within 7 days of injury. We calculated absolute changes in volume of intraparenchymal, extra-axial, intraventricular, and total intracranial hemorrhage (ICH) between scans, and compared volume of hemorrhagic progression, proportion of patients with significant degree of progression (>25% of initial volume), proportion with new ICH on follow-up CT, as well as clinical course and outcomes. A total of 316 patients were included (158 APAC users; 158 controls). The mean volume of progression was significantly higher in the APAC group for extra-axial (3.1 vs. 1.3 mL, p = 0.01), but not intraparenchymal (3.8 vs. 4.6 mL, p = 0.65), intraventricular (0.2 vs. 0.0 mL, p = 0.79), or total intracranial hemorrhage (ICH; 7.0 vs. 6.0 mL, p = 0.08). More patients had significant hemorrhage growth (54.1 vs. 37.0%, p = 0.003) and delayed ICH (4 of 18 vs. none; p = 0.04) in the APAC group compared with controls, but this was not associated with differences in length of stay (LOS), rates of neurosurgical intervention, mortality or Glasgow Outcome Scale Extended (GOS-E) score at 6 months. Pre-injury use of antithrombotic agents was associated with greater expansion of extra-axial lesions, higher rates of significant hemorrhagic progression, and higher risk of delayed traumatic ICH, but this was not associated with worse clinical course or functional outcomes.
  •  
42.
  • Mathieu, François, et al. (författare)
  • Relationship Between Measures of Cerebrovascular Reactivity and Intracranial Lesion Progression in Acute TBI Patients : an Exploratory Analysis.
  • 2020
  • Ingår i: Neurocritical Care. - : Springer. - 1541-6933 .- 1556-0961. ; 32:2, s. 373-382
  • Tidskriftsartikel (refereegranskat)abstract
    • BACKGROUND: Failure of cerebral autoregulation and progression of intracranial lesion have both been shown to contribute to poor outcome in patients with acute traumatic brain injury (TBI), but the interplay between the two phenomena has not been investigated. Preliminary evidence leads us to hypothesize that brain tissue adjacent to primary injury foci may be more vulnerable to large fluctuations in blood flow in the absence of intact autoregulatory mechanisms. The goal of this study was therefore to assess the influence of cerebrovascular reactivity measures on radiological lesion expansion in a cohort of patients with acute TBI.METHODS: We conducted a retrospective cohort analysis on 50 TBI patients who had undergone high-frequency multimodal intracranial monitoring and for which at least two brain computed tomography (CT) scans had been performed in the acute phase of injury. We first performed univariate analyses on the full cohort to identify non-neurophysiological factors (i.e., initial lesion volume, timing of scan, coagulopathy) associated with traumatic lesion growth in this population. In a subset analysis of 23 patients who had intracranial recording data covering the period between the initial and repeat CT scan, we then correlated changes in serial volumetric lesion measurements with cerebrovascular reactivity metrics derived from the pressure reactivity index (PRx), pulse amplitude index (PAx), and RAC (correlation coefficient between the pulse amplitude of intracranial pressure and cerebral perfusion pressure). Using multivariate methods, these results were subsequently adjusted for the non-neurophysiological confounders identified in the univariate analyses.RESULTS: We observed significant positive linear associations between the degree of cerebrovascular reactivity impairment and progression of pericontusional edema. The strongest correlations were observed between edema progression and the following indices of cerebrovascular reactivity between sequential scans: % time PRx > 0.25 (r = 0.69, p = 0.002) and % time PAx > 0.25 (r = 0.64, p = 0.006). These associations remained significant after adjusting for initial lesion volume and mean cerebral perfusion pressure. In contrast, progression of the hemorrhagic core and extra-axial hemorrhage volume did not appear to be strongly influenced by autoregulatory status.CONCLUSIONS: Our preliminary findings suggest a possible link between autoregulatory failure and traumatic edema progression, which warrants re-evaluation in larger-scale prospective studies.
  •  
43.
  • Mathieu, François, et al. (författare)
  • Relationship between Measures of CerebrovascularReactivity and Intracranial Lesion Progressionin Acute Traumatic Brain Injury Patients:A CENTER-TBI Study
  • 2020
  • Ingår i: Journal of Neurotrauma. - : Mary Ann Liebert. - 0897-7151 .- 1557-9042. ; 37:13, s. 1556-1565
  • Tidskriftsartikel (refereegranskat)abstract
    • Failure of cerebral autoregulation has been linked to unfavorable outcome after traumatic brain injury (TBI). Preliminary evidence from a small, retrospective, single-center analysis suggests that autoregulatory dysfunction may be associated with traumatic lesion expansion, particularly for pericontusional edema. The goal of this study was to further explore these associations using prospective, multi-center data from the Collaborative European Neurotrauma Effectiveness Research in TBI (CENTER-TBI) and to further explore the relationship between autoregulatory failure, lesion progression, and patient outcome. A total of 88 subjects from the CENTER-TBI High Resolution ICU Sub-Study cohort were included. All patients had an admission computed tomography (CT) scan and early repeat scan available, as well as high-frequency neurophysiological recordings covering the between-scan interval. Using a novel, semiautomated approach at lesion segmentation, we calculated absolute changes in volume of contusion core, pericontusional edema, and extra-axial hemorrhage between the imaging studies. We then evaluated associations between cerebrovascular reactivity metrics and radiological lesion progression using mixed-model regression. Analyses were adjusted for baseline covariates and non-neurophysiological factors associated with lesion growth using multi-variate methods. Impairment in cerebrovascular reactivity was significantly associated with progression of pericontusional edema and, to a lesser degree, intraparenchymal hemorrhage. In contrast, there were no significant associations with extra-axial hemorrhage. The strongest relationships were observed between RAC-based metrics and edema formation. Pulse amplitude index showed weaker, but consistent, associations with contusion growth. Cerebrovascular reactivity metrics remained strongly associated with lesion progression after taking into account contributions from non-neurophysiological factors and mean cerebral perfusion pressure. Total hemorrhagic core and edema volumes on repeat CT were significantly larger in patients who were deceased at 6 months, and the amount of edema was greater in patients with an unfavourable outcome (Glasgow Outcome Scale-Extended 1–4). Our study suggests associations between autoregulatory failure, traumatic edema progression, and poor outcome. This is in keeping with findings from a single-center retrospective analysis, providing multi-center prospective data to support those results.
  •  
44.
  • Nandi, Saikat, et al. (författare)
  • Generation of entanglement using a short-wavelength seeded free-electron laser
  • 2024
  • Ingår i: SCIENCE ADVANCES. - 2375-2548. ; 10:16
  • Tidskriftsartikel (refereegranskat)abstract
    • Quantum entanglement between the degrees of freedom encountered in the classical world is challenging to observe due to the surrounding environment. To elucidate this issue, we investigate the entanglement generated over ultrafast timescales in a bipartite quantum system comprising two massive particles: a free-moving photoelectron, which expands to a mesoscopic length scale, and a light-dressed atomic ion, which represents a hybrid state of light and matter. Although the photoelectron spectra are measured classically, the entanglement allows us to reveal information about the dressed-state dynamics of the ion and the femtosecond extreme ultraviolet pulses delivered by a seeded free-electron laser. The observed generation of entanglement is interpreted using the time-dependent von Neumann entropy. Our results unveil the potential for using short-wavelength coherent light pulses from free-electron lasers to generate entangled photoelectron and ion systems for studying spooky action at a distance.
  •  
45.
  • Nandi, Saikat, et al. (författare)
  • Observation of Rabi dynamics with a short-wavelength free-electron laser
  • 2022
  • Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 608:7923
  • Tidskriftsartikel (refereegranskat)abstract
    • Rabi oscillations are periodic modulations of populations in two-level systems interacting with a time-varying field(1). They are ubiquitous in physics with applications in different areas such as photonics(2), nano-electronics(3), electron microscopy(4) and quantum information(5). While the theory developed by Rabi was intended for fermions in gyrating magnetic fields, Autler and Townes realized that it could also be used to describe coherent light-matter interactions within the rotating-wave approximation(6). Although intense nanometre-wavelength light sources have been available for more than a decade(7-9), Rabi dynamics at such short wavelengths has not been directly observed. Here we show that femtosecond extreme-ultraviolet pulses from a seeded free-electron laser(10) can drive Rabi dynamics between the ground state and an excited state in helium atoms. The measured photoelectron signal reveals an Autler-Townes doublet and an avoided crossing, phenomena that are both fundamental to coherent atom-field interactions(11). Using an analytical model derived from perturbation theory on top of the Rabi model, we find that the ultrafast build-up of the doublet structure carries the signature of a quantum interference effect between resonant and non-resonant photoionization pathways. Given the recent availability of intense attosecond(12) and few-femtosecond(13) extreme-ultraviolet pulses, our results unfold opportunities to carry out ultrafast manipulation of coherent processes at short wavelengths using free-electron lasers.
  •  
46.
  • Nandi, Saikat, et al. (författare)
  • Unraveling Rabi dynamics with a seeded FEL at XUV wavelength
  • 2023
  • Ingår i: 2023 Conference on Lasers and Electro-Optics Europe and European Quantum Electronics Conference, CLEO/Europe-EQEC 2023. - 9798350345995
  • Konferensbidrag (refereegranskat)abstract
    • Rabi oscillations, a prominent feature of coherent light-matter interaction arise when a two-level system interacts periodically with an external electromagnetic field [1]. Despite being a cornerstone in quantum physics, they are usually studied in the long-wavelength region, ranging from mid-infrared to visible. Here, we demonstrate that intense femtosecond extreme-ultraviolet (XUV) pulses from FERMI seeded free-electron laser [2] can drive Rabi oscillations between the two levels: 1s2 and 1s4p in helium.
  •  
47.
  • Oldenhof, Martijn, et al. (författare)
  • Industry-Scale Orchestrated Federated Learning for Drug Discovery
  • 2023
  • Ingår i: Proceedings of the 37th AAAI Conference on Artificial Intelligence, AAAI 2023. ; 37, s. 15576-15584
  • Konferensbidrag (refereegranskat)abstract
    • To apply federated learning to drug discovery we developed a novel platform in the context of European Innovative Medicines Initiative (IMI) project MELLODDY (grant n°831472), which was comprised of 10 pharmaceutical companies, academic research labs, large industrial companies and startups. The MELLODDY platform was the first industry-scale platform to enable the creation of a global federated model for drug discovery without sharing the confidential data sets of the individual partners. The federated model was trained on the platform by aggregating the gradients of all contributing partners in a cryptographic, secure way following each training iteration. The platform was deployed on an Amazon Web Services (AWS) multi-account architecture running Kubernetes clusters in private subnets. Organisationally, the roles of the different partners were codified as different rights and permissions on the platform and administrated in a decentralized way. The MELLODDY platform generated new scientific discoveries which are described in a companion paper.
  •  
48.
  • Olson, Nathan D., et al. (författare)
  • precisionFDA Truth Challenge V2: Calling variants from short- and long-reads in difficult-to-map regions
  • 2020
  • Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
    • 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 Technologies). Submissions were evaluated following best practices for benchmarking small variants with the new GIAB benchmark sets and genome stratifications. Challenge submissions included a number of innovative methods for all three technologies, with graph-based and machine-learning methods scoring best for short-read and long-read datasets, respectively. New methods out-performed the 2016 Truth Challenge winners, and new machine-learning approaches combining multiple sequencing technologies performed particularly well. Recent developments in sequencing and variant calling have enabled benchmarking variants in challenging genomic regions, paving the way for the identification of previously unknown clinically relevant variants.
  •  
49.
  • Olson, Nathan D., et al. (författare)
  • PrecisionFDA Truth Challenge V2: Calling variants from short and long reads in difficult-to-map regions
  • 2022
  • Ingår i: Cell Genomics. - : Elsevier BV. - 2666-979X. ; 2:5, s. 1-12
  • Tidskriftsartikel (refereegranskat)abstract
    • The precisionFDA Truth Challenge V2 aimed to assess the state of the art of variant calling in challenging genomic regions. Starting with FASTQs, 20 challenge participants applied their variant-calling pipelines and submitted 64 variant call sets for one or more sequencing technologies (Illumina, PacBio HiFi, and Oxford Nanopore Technologies). Submissions were evaluated following best practices for benchmarking small variants with updated Genome in a Bottle benchmark sets and genome stratifications. Challenge submissions included numerous innovative methods, with graph-based and machine learning methods scoring best for short-read and long-read datasets, respectively. With machine learning approaches, combining multiple sequencing technologies performed particularly well. Recent developments in sequencing and variant calling have enabled benchmarking variants in challenging genomic regions, paving the way for the identification of previously unknown clinically relevant variants.
  •  
50.
  • Perrot, Nicolas, et al. (författare)
  • Genetic and In Vitro Inhibition of PCSK9 and Calcific Aortic Valve Stenosis
  • 2020
  • Ingår i: JACC: Basic to Translational Science. - : Elsevier BV. - 2452-302X. ; 5:7, s. 649-661
  • Tidskriftsartikel (refereegranskat)abstract
    • The authors investigated whether PCSK9 inhibition could represent a therapeutic strategy in calcific aortic valve stenosis (CAVS). A meta-analysis of 10 studies was performed to determine the impact of the PCSK9 R46L variant on CAVS, and the authors found that CAVS was less prevalent in carriers of this variant (odds ratio: 0.80 [95% confidence interval: 0.70 to 0.91]; p = 0.0011) compared with noncarriers. PCSK9 expression was higher in the aortic valves of patients CAVS compared with control patients. In human valve interstitials cells submitted to a pro-osteogenic medium, PCSK9 levels increased and a PCSK9 neutralizing antibody significantly reduced calcium accumulation.
  •  
Skapa referenser, mejla, bekava och länka
  • Resultat 1-50 av 67
Typ av publikation
tidskriftsartikel (58)
konferensbidrag (4)
forskningsöversikt (3)
annan publikation (1)
bokkapitel (1)
Typ av innehåll
refereegranskat (63)
övrigt vetenskapligt/konstnärligt (4)
Författare/redaktör
Menon, David K. (10)
Stocchetti, Nino (9)
Koskinen, Lars-Owe D ... (8)
Ercole, Ari (8)
Feifel, Raimund (6)
Chang-Claude, Jenny (4)
visa fler...
Berndt, Sonja I (4)
Brenner, Hermann (4)
Thibodeau, Stephen N (4)
Chan, Andrew T. (4)
Figueiredo, Jane C. (4)
Hoffmeister, Michael (4)
Jenkins, Mark A. (4)
Moreno, Victor (4)
Newcomb, Polly A. (4)
Peters, Ulrike (4)
Campbell, Peter T. (4)
Orešič, Matej, 1967- (4)
Linares, Mathieu (4)
L'Huillier, Anne (4)
Wang, Kai (3)
Wolk, Alicja (3)
Albanes, Demetrius (3)
Giles, Graham G (3)
Pruulmann-Vengerfeld ... (3)
Arndt, Volker (3)
Buchanan, Daniel D. (3)
Casey, Graham (3)
Gruber, Stephen B. (3)
Gsur, Andrea (3)
Gunter, Marc J. (3)
Harrison, Tabitha A. (3)
Huyghe, Jeroen R. (3)
Joshi, Amit D. (3)
Li, Li (3)
Ogino, Shuji (3)
Sakoda, Lori C. (3)
Slattery, Martha L. (3)
Ulrich, Cornelia M. (3)
van Guelpen, Bethany (3)
White, Emily (3)
Woods, Michael O. (3)
Wu, Anna H. (3)
Hsu, Li (3)
Drew, David A. (3)
Zaidi, Syed H. (3)
Lindblom, Annika (3)
Offit, Kenneth (3)
Pharoah, Paul D. P. (3)
Smielewski, Peter (3)
visa färre...
Lärosäte
Karolinska Institutet (18)
Umeå universitet (17)
Lunds universitet (16)
Uppsala universitet (13)
Göteborgs universitet (11)
Örebro universitet (7)
visa fler...
Stockholms universitet (6)
Linköpings universitet (6)
Kungliga Tekniska Högskolan (4)
Chalmers tekniska högskola (4)
Malmö universitet (3)
Sveriges Lantbruksuniversitet (2)
Högskolan i Gävle (1)
IVL Svenska Miljöinstitutet (1)
visa färre...
Språk
Engelska (67)
Forskningsämne (UKÄ/SCB)
Medicin och hälsovetenskap (32)
Naturvetenskap (31)
Lantbruksvetenskap (3)
Samhällsvetenskap (3)
Teknik (1)
Humaniora (1)

År

Kungliga biblioteket hanterar dina personuppgifter i enlighet med EU:s dataskyddsförordning (2018), GDPR. Läs mer om hur det funkar här.
Så här hanterar KB dina uppgifter vid användning av denna tjänst.

 
pil uppåt Stäng

Kopiera och spara länken för att återkomma till aktuell vy