| 1. |
- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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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.
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| 2. |
- Elhag, Sara, et al.
(författare)
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Differences in Cell-Intrinsic Inflammatory Programs of Yolk Sac and Bone Marrow Macrophages
- 2021
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Ingår i: Cells. - : MDPI AG. - 2073-4409. ; 10:12
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Tidskriftsartikel (refereegranskat)abstract
- Background: Tissue-resident macrophages have mixed developmental origins. They derive in variable extent from yolk sac (YS) hematopoiesis during embryonic development. Bone marrow (BM) hematopoietic progenitors give rise to tissue macrophages in postnatal life, and their contribution increases upon organ injury. Since the phenotype and functions of macrophages are modulated by the tissue of residence, the impact of their origin and developmental paths has remained incompletely understood. Methods: In order to decipher cell-intrinsic macrophage programs, we immortalized hematopoietic progenitors from YS and BM using conditional HoxB8, and carried out an in-depth functional and molecular analysis of differentiated macrophages. Results: While YS and BM macrophages demonstrate close similarities in terms of cellular growth, differentiation, cell death susceptibility and phagocytic properties, they display differences in cell metabolism, expression of inflammatory markers and inflammasome activation. Reduced abundance of PYCARD (ASC) and CASPASE-1 proteins in YS macrophages abrogated interleukin-1 beta production in response to canonical and non-canonical inflammasome activation. Conclusions: Macrophage ontogeny is associated with distinct cellular programs and immune response. Our findings contribute to the understanding of the regulation and programming of macrophage functions.
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| 3. |
- Koenig, Julian, et al.
(författare)
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Cortical thickness and resting-state cardiac function across the lifespan : A cross-sectional pooled mega-analysis
- 2021
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Ingår i: Psychophysiology. - : Wiley. - 0048-5772 .- 1469-8986 .- 1540-5958. ; 58:7
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Tidskriftsartikel (refereegranskat)abstract
- Understanding the association between autonomic nervous system [ANS] function and brain morphology across the lifespan provides important insights into neurovisceral mechanisms underlying health and disease. Resting-state ANS activity, indexed by measures of heart rate [HR] and its variability [HRV] has been associated with brain morphology, particularly cortical thickness [CT]. While findings have been mixed regarding the anatomical distribution and direction of the associations, these inconsistencies may be due to sex and age differences in HR/HRV and CT. Previous studies have been limited by small sample sizes, which impede the assessment of sex differences and aging effects on the association between ANS function and CT. To overcome these limitations, 20 groups worldwide contributed data collected under similar protocols of CT assessment and HR/HRV recording to be pooled in a mega-analysis (N = 1,218 (50.5% female), mean age 36.7 years (range: 12–87)). Findings suggest a decline in HRV as well as CT with increasing age. CT, particularly in the orbitofrontal cortex, explained additional variance in HRV, beyond the effects of aging. This pattern of results may suggest that the decline in HRV with increasing age is related to a decline in orbitofrontal CT. These effects were independent of sex and specific to HRV; with no significant association between CT and HR. Greater CT across the adult lifespan may be vital for the maintenance of healthy cardiac regulation via the ANS—or greater cardiac vagal activity as indirectly reflected in HRV may slow brain atrophy. Findings reveal an important association between CT and cardiac parasympathetic activity with implications for healthy aging and longevity that should be studied further in longitudinal research.
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| 4. |
- Alimena, Juliette, et al.
(författare)
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Searching for long-lived particles beyond the Standard Model at the Large Hadron Collider
- 2020
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Ingår i: Journal of Physics G. - : IOP Publishing. - 0954-3899 .- 1361-6471. ; 47:9
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Tidskriftsartikel (refereegranskat)abstract
- Particles beyond the Standard Model (SM) can generically have lifetimes that are long compared to SM particles at the weak scale. When produced at experiments such as the Large Hadron Collider (LHC) at CERN, these long-lived particles (LLPs) can decay far from the interaction vertex of the primary proton-proton collision. Such LLP signatures are distinct from those of promptly decaying particles that are targeted by the majority of searches for new physics at the LHC, often requiring customized techniques to identify, for example, significantly displaced decay vertices, tracks with atypical properties, and short track segments. Given their non-standard nature, a comprehensive overview of LLP signatures at the LHC is beneficial to ensure that possible avenues of the discovery of new physics are not overlooked. Here we report on the joint work of a community of theorists and experimentalists with the ATLAS, CMS, and LHCb experiments-as well as those working on dedicated experiments such as MoEDAL, milliQan, MATHUSLA, CODEX-b, and FASER-to survey the current state of LLP searches at the LHC, and to chart a path for the development of LLP searches into the future, both in the upcoming Run 3 and at the high-luminosity LHC. The work is organized around the current and future potential capabilities of LHC experiments to generally discover new LLPs, and takes a signature-based approach to surveying classes of models that give rise to LLPs rather than emphasizing any particular theory motivation. We develop a set of simplified models; assess the coverage of current searches; document known, often unexpected backgrounds; explore the capabilities of proposed detector upgrades; provide recommendations for the presentation of search results; and look towards the newest frontiers, namely high-multiplicity 'dark showers', highlighting opportunities for expanding the LHC reach for these signals.
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| 5. |
- Calore, Francesca, et al.
(författare)
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3D template-based Fermi-LAT constraints on the diffuse supernova axion-like particle background
- 2022
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Ingår i: Physical Review D. - 2470-0010 .- 2470-0029. ; 105:6
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Tidskriftsartikel (refereegranskat)abstract
- Axion-like particles (ALPs) may be abundantly produced in core-collapse (CC) supernovae (SNe); hence, the cumulative signal from all past supernova (SN) events can create a diffuse flux peaked at energies of about 25 MeV. We improve upon the modeling of the ALPs flux by including a set of CC SN models with different progenitor masses, as well as the effects of failed CC SNe, which yield the formation of black holes instead of explosions. Relying on the coupling strength of ALPs to photons and the related Primakoff process, the diffuse SN ALP flux is converted into gamma rays while traversing the magnetic field of the Milky Way. The spatial morphology of this signal is expected to follow the shape of the Galactic magnetic field lines. We make use of this via a template-based analysis that utilizes 12 years of Fermi-LAT data in the energy range from 50 MeV to 500 GeV. In our benchmark case of the realization of astrophysical and cosmological parameters, we find an upper limit of gaγ≲3.76×10−11 GeV−1 at a 95% confidence level for ma≪10−11 eV, while we find that systematic deviations from this benchmark scenario induce an uncertainty as large as about a factor of two. Our result slightly improves the CAST bound, while still being a factor of six (baseline scenario) weaker than the SN1987A gamma-ray burst limit.
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| 6. |
- Eichhorst, B., et al.
(författare)
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First-Line Venetoclax Combinations in Chronic Lymphocytic Leukemia.
- 2023
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Ingår i: New England Journal of Medicine. - : MASSACHUSETTS MEDICAL SOC. - 0028-4793 .- 1533-4406. ; 388:19, s. 1739-1754
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Tidskriftsartikel (refereegranskat)abstract
- Background Randomized trials of venetoclax plus anti-CD20 antibodies as first-line treatment in fit patients (i.e., those with a low burden of coexisting conditions) with advanced chronic lymphocytic leukemia (CLL) have been lacking. Methods In a phase 3, open-label trial, we randomly assigned, in a 1:1:1:1 ratio, fit patients with CLL who did not have TP53 aberrations to receive six cycles of chemoimmunotherapy (fludarabine-cyclophosphamide-rituximab or bendamustine-rituximab) or 12 cycles of venetoclax-rituximab, venetoclax-obinutuzumab, or venetoclax-obinutuzumab-ibrutinib. Ibrutinib was discontinued after two consecutive measurements of undetectable minimal residual disease or could be extended. The primary end points were undetectable minimal residual disease (sensitivity,
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| 7. |
- Erhardt, Tobias, et al.
(författare)
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High-resolution aerosol concentration data from the Greenland NorthGRIP and NEEM deep ice cores
- 2022
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Ingår i: Earth System Science Data. - : Copernicus GmbH. - 1866-3508 .- 1866-3516. ; 14:3, s. 1215-1231
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Tidskriftsartikel (refereegranskat)abstract
- Records of chemical impurities from ice cores enable us to reconstruct the past deposition of aerosols onto polar ice sheets and alpine glaciers. Through this they allow us to gain insight into changes of the source, transport and deposition processes that ultimately determine the deposition flux at the coring location. However, the low concentrations of the aerosol species in the ice and the resulting high risk of contamination pose a formidable analytical challenge, especially if long, continuous and highly resolved records are needed. Continuous flow analysis, CFA, the continuous melting, decontamination and analysis of ice-core samples has mostly overcome this issue and has quickly become the de facto standard to obtain high-resolution aerosol records from ice cores after its inception at the University of Bern in the mid-1990s.Here, we present continuous records of calcium (Ca2+), sodium (Na+), ammonium (NH+4), nitrate (NO-3) and electrolytic conductivity at 1 mm depth resolution from the NGRIP (North Greenland Ice Core Project) and NEEM (North Greenland Eemian Ice Drilling) ice cores produced by the Bern Continuous Flow Analysis group in the years 2000 to 2011 (Erhardt et al., 2021). Both of the records were previously used in a number of studies but were never published in full 1 mm resolution. Alongside the 1 mm datasets we provide decadal averages, a detailed description of the methods, relevant references, an assessment of the quality of the data and its usable resolution. Along the way we will also give some historical context on the development of the Bern CFA system.
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| 8. |
- Erhardt, Tobias, et al.
(författare)
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High-resolution aerosol data from the top 3.8kyr of the East Greenland Ice coring Project (EGRIP) ice core
- 2023
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Ingår i: Earth System Science Data. - 1866-3508. ; 15:11, s. 5079-5091
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Tidskriftsartikel (refereegranskat)abstract
- Here we present the high-resolution continuous flow analysis (CFA) data from the top 479m of the East Greenland Ice coring Project (EGRIP) ice core covering the past 3.8kyr. The data consist of 1mm depth-resolution profiles of calcium, sodium, ammonium, nitrate, and electrolytic conductivity as well as decadal averages of these profiles. The nominally 1mm data represent an oversampling of the record as the true resolution is limited by the analytical setup to approximately 1cm. Alongside the data we provide a description of the measurement setup, procedures, the relevant references for the specific methods as well as an assessment of the precision of the measurements, the sample-to-depth assignment, and the depth and temporal resolution of the data set. The error in absolute depth assignment of the data may be on the order of 2cm; however, relative depth offsets between the records of the individual species are only on the order of 1mm. The presented data have sub-annual resolution over the entire depth range and have already formed part of the data for an annually layer-counted timescale for the EGRIP ice core used to improve and revise the multi-core Greenland ice-core chronology (GICC05) to a new version, GICC21 . The data are available in full 1mm resolution and decadal averages on PANGAEA (10.1594/PANGAEA.945293, ).
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| 9. |
- Fhager, Johan, et al.
(författare)
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The hairdex quality of life instrument : a translation and psychometric validation in patients with alopecia areata
- 2023
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Ingår i: Skin Health and Disease. - : John Wiley & Sons. - 2690-442X. ; 3:3
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Tidskriftsartikel (refereegranskat)abstract
- Background: The German Hairdex quality of life (QoL) instrument is specific to hair and scalp diseases, developed for self-rating and consists of 48 statements divided into five domains: Symptoms, Functioning, Emotions, Self-confidence and Stigmatisation. There was a need of a Swedish reliability tested, validated hair and scalp specific QoL instrument why the German Hairdex was chosen to be translated and reliability tested in a systematic way.Objectives: To make a translation, a reliability test of stability, and validation of the German Hairdex QoL instrument among 100 Swedish patients with a dermatological ICD-10 diagnosis of alopecia areata (AA).Methods: An eight-step method by Gudmundsson was used as a model with a forward and backward translation and with comments from an expert panel. A statistical test–retest (ICC (2,1)) analysis was made, followed by an internal consistency analysis. A comparison between the German and Swedish Hairdex-S constructs by a principal component analysis was performed.Results: The Hairdex-S was very well accepted by patients. The ICC(2,1) test–retest showed a good to excellent correlation of 0.91 (CI [0.85–0.95]). Internal consistency was α = 0.92. Like the original Hairdex, Hairdex-S showed good factorability with a Kaiser–Meyer–Olkin measure of 0.82 and with one component explaining 70% of the variance: original Hairdex instrument (69%). When tested on patients with AA, the domains Functioning and Emotions had the strongest loadings, followed by Stigmatisation and Self-confidence. Younger AA patients at self-assessment and patients who reported to be younger at the onset of AA, scored statistically significantly higher on the Hairdex-S, indicating an overall lower QoL on domains Emotions and Functioning, respectively.Conclusions: The Hairdex-S is very well accepted by AA patients, shows very good psychometric properties, and a very good agreement with the original Hairdex. The Swedish Hairdex instrument can be recommended for evaluation of patients QoL as well as for research purposes.
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| 10. |
- Galle, Bo, 1952, et al.
(författare)
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A multi-purpose, multi-rotor drone system for long-range and high-altitude volcanic gas plume measurements
- 2021
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Ingår i: Atmospheric Measurement Techniques. - : Copernicus GmbH. - 1867-1381 .- 1867-8548. ; 14:6, s. 4255-4277
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Tidskriftsartikel (refereegranskat)abstract
- A multi-rotor drone has been adapted for studies of volcanic gas plumes. This adaptation includes improved capacity for high-altitude and long-range, real-time SO2 concentration monitoring, long-range manual control, remotely activated bag sampling and plume speed measurement capability. The drone is capable of acting as a stable platform for various instrument configurations, including multi-component gas analysis system (MultiGAS) instruments for in situ measurements of SO2, H2S, and CO2 concentrations in the gas plume and portable differential optical absorption spectrometer (MobileDOAS) instruments for spectroscopic measurement of total SO2 emission rate, remotely controlled gas sampling in bags and sampling with gas denuders for posterior analysis on the ground of isotopic composition and halogens. The platform we present was field-tested during three campaigns in Papua New Guinea: in 2016 at Tavurvur, Bagana and Ulawun volcanoes, in 2018 at Tavurvur and Langila volcanoes and in 2019 at Tavurvur and Manam volcanoes, as well as in Mt. Etna in Italy in 2017. This paper describes the drone platform and the multiple payloads, the various measurement strategies and an algorithm to correct for different response times of MultiGAS sensors. Specifically, we emphasize the need for an adaptive flight path, together with live data transmission of a plume tracer (such as SO2 concentration) to the ground station, to ensure optimal plume interception when operating beyond the visual line of sight. We present results from a comprehensive plume characterization obtained during a field deployment at Manam volcano in May 2019. The Papua New Guinea region, and particularly Manam volcano, has not been extensively studied for volcanic gases due to its remote location, inaccessible summit region and high level of volcanic activity. We demonstrate that the combination of a multi-rotor drone with modular payloads is a versatile solution to obtain the flux and composition of volcanic plumes, even for the case of a highly active volcano with a high-altitude plume such as Manam. Drone-based measurements offer a valuable solution to volcano research and monitoring applications and provide an alternativespan idCombining double low line"page4256"/> and complementary method to ground-based and direct sampling of volcanic gases.
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