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- 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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| 5. |
- Bengtsson, Alexander, et al.
(författare)
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Characterization and modeling of acousto-optic signal strengths in highly scattering media
- 2019
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Ingår i: Biomedical Optics Express. - 2156-7085. ; 10:11, s. 5565-5584
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Tidskriftsartikel (refereegranskat)abstract
- Ultrasound optical tomography (UOT) is an imaging technique based on the acousto-optic effect that can perform optical imaging with ultrasound resolution inside turbid media, and is thus interesting for biomedical applications, e.g. for assessing tissue blood oxygenation. In this paper, we present near background free measurements of UOT signal strengths using slow light filter signal detection. We carefully analyze each part of our experimental setup and match measured signal strengths with calculations based on diffusion theory. This agreement between experiment and theory allows us to assert the deep tissue imaging potential of similar to 5 cm for UOT of real human tissues predicted by previous theoretical studies [Biomed. Opt. Express 8, 4523 (2017)] with greater confidence, and indicate that future theoretical analysis of optimized UOT systems can be expected to be reliable. (C) 2019 Optical Society of America under the terms of the OSA Open Access Publishing Agreement
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| 6. |
- Charman, Tony, et al.
(författare)
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The EU-AIMS Longitudinal European Autism Project (LEAP) : clinical characterisation.
- 2017
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Ingår i: Molecular Autism. - : Springer Science and Business Media LLC. - 2040-2392. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: The EU-AIMS Longitudinal European Autism Project (LEAP) is to date the largest multi-centre, multi-disciplinary observational study on biomarkers for autism spectrum disorder (ASD). The current paper describes the clinical characteristics of the LEAP cohort and examines age, sex and IQ differences in ASD core symptoms and common co-occurring psychiatric symptoms. A companion paper describes the overall design and experimental protocol and outlines the strategy to identify stratification biomarkers.METHODS: From six research centres in four European countries, we recruited 437 children and adults with ASD and 300 controls between the ages of 6 and 30 years with IQs varying between 50 and 148. We conducted in-depth clinical characterisation including a wide range of observational, interview and questionnaire measures of the ASD phenotype, as well as co-occurring psychiatric symptoms.RESULTS: The cohort showed heterogeneity in ASD symptom presentation, with only minimal to moderate site differences on core clinical and cognitive measures. On both parent-report interview and questionnaire measures, ASD symptom severity was lower in adults compared to children and adolescents. The precise pattern of differences varied across measures, but there was some evidence of both lower social symptoms and lower repetitive behaviour severity in adults. Males had higher ASD symptom scores than females on clinician-rated and parent interview diagnostic measures but not on parent-reported dimensional measures of ASD symptoms. In contrast, self-reported ASD symptom severity was higher in adults compared to adolescents, and in adult females compared to males. Higher scores on ASD symptom measures were moderately associated with lower IQ. Both inattentive and hyperactive/impulsive ADHD symptoms were lower in adults than in children and adolescents, and males with ASD had higher levels of inattentive and hyperactive/impulsive ADHD symptoms than females.CONCLUSIONS: The established phenotypic heterogeneity in ASD is well captured in the LEAP cohort. Variation both in core ASD symptom severity and in commonly co-occurring psychiatric symptoms were systematically associated with sex, age and IQ. The pattern of ASD symptom differences with age and sex also varied by whether these were clinician ratings or parent- or self-reported which has important implications for establishing stratification biomarkers and for their potential use as outcome measures in clinical trials.
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| 7. |
- Dewey, Marc, et al.
(författare)
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Clinical quantitative cardiac imaging for the assessment of myocardial ischaemia
- 2020
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Ingår i: Nature Reviews Cardiology. - : Springer Nature. - 1759-5002 .- 1759-5010. ; 17:7, s. 427-450
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Tidskriftsartikel (refereegranskat)abstract
- Cardiac imaging has a pivotal role in the prevention, diagnosis and treatment of ischaemic heart disease. SPECT is most commonly used for clinical myocardial perfusion imaging, whereas PET is the clinical reference standard for the quantification of myocardial perfusion. MRI does not involve exposure to ionizing radiation, similar to echocardiography, which can be performed at the bedside. CT perfusion imaging is not frequently used but CT offers coronary angiography data, and invasive catheter-based methods can measure coronary flow and pressure. Technical improvements to the quantification of pathophysiological parameters of myocardial ischaemia can be achieved. Clinical consensus recommendations on the appropriateness of each technique were derived following a European quantitative cardiac imaging meeting and using a real-time Delphi process. SPECT using new detectors allows the quantification of myocardial blood flow and is now also suited to patients with a high BMI. PET is well suited to patients with multivessel disease to confirm or exclude balanced ischaemia. MRI allows the evaluation of patients with complex disease who would benefit from imaging of function and fibrosis in addition to perfusion. Echocardiography remains the preferred technique for assessing ischaemia in bedside situations, whereas CT has the greatest value for combined quantification of stenosis and characterization of atherosclerosis in relation to myocardial ischaemia. In patients with a high probability of needing invasive treatment, invasive coronary flow and pressure measurement is well suited to guide treatment decisions. In this Consensus Statement, we summarize the strengths and weaknesses as well as the future technological potential of each imaging modality.
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| 8. |
- Erickson, Brittany A., et al.
(författare)
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Incorporating Full Elastodynamic Effects and Dipping Fault Geometries in Community Code Verification Exercises for Simulations of Earthquake Sequences and Aseismic Slip (SEAS)
- 2023
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Ingår i: Bulletin of The Seismological Society of America (BSSA). - : SEISMOLOGICAL SOC AMER. - 0037-1106 .- 1943-3573. ; 113:2, s. 499-523
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Tidskriftsartikel (refereegranskat)abstract
- Numerical modeling of earthquake dynamics and derived insight for seismic hazard relies on credible, reproducible model results. The sequences of earthquakes and aseismic slip (SEAS) initiative has set out to facilitate community code comparisons, and verify and advance the next generation of physics-based earthquake models that reproduce all phases of the seis-mic cycle. With the goal of advancing SEAS models to robustly incorporate physical and geo-metrical complexities, here we present code comparison results from two new benchmark problems: BP1-FD considers full elastodynamic effects, and BP3-QD considers dipping fault geometries. Seven and eight modeling groups participated in BP1-FD and BP3-QD, respectively, allowing us to explore these physical ingredients across multiple codes and better understand associated numerical considerations. With new comparison metrics, we find that numerical resolution and computational domain size are critical parameters to obtain matching results. Codes for BP1-FD implement different criteria for switching between quasi-static and dynamic solvers, which require tuning to obtain matching results. In BP3-QD, proper remote boundary conditions consistent with specified rigid body translation are required to obtain matching surface displacements. With these numerical and mathematical issues resolved, we obtain excellent quantitative agreements among codes in earthquake interevent times, event moments, and coseismic slip, with reasonable agreements made in peak slip rates and rupture arrival time. We find that including full inertial effects generates events with larger slip rates and rupture speeds compared to the quasi-dynamic counterpart. For BP3-QD, both dip angle and sense of motion (thrust versus normal faulting) alter ground motion on the hanging and foot walls, and influence event patterns, with some sequences exhibiting similar-size character-istic earthquakes, and others exhibiting different-size events. These findings underscore the importance of considering full elastodynamics and nonvertical dip angles in SEAS models, as both influence short-and long-term earthquake behavior and are relevant to seismic hazard.
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| 9. |
- Facio, Jorge, et al.
(författare)
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Engineering a pure Dirac regime in ZrTe5
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Ingår i: SciPost Physics. - 2542-4653.
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Real-world topological semimetals typically exhibit Dirac and Weyl nodes that coexist with trivial Fermi pockets. This tends to mask the physics of the relativistic quasiparticles. Using the example of ZrTe5, we show that strain provides a powerful tool for in-situ tuning of the band structure such that all trivial pockets are pushed far away from the Fermi energy, but only for a certain range of Van der Waals gaps. Our results naturally reconcile contradicting reports on the presence or absence of additional pockets in ZrTe5, and provide a clear map of where to find a pure three-dimensional Dirac semimetallic phase in the structural parameter space of the material.
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| 10. |
- Facio, Jorge I., et al.
(författare)
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Engineering a pure Dirac regime in ZrTe5
- 2023
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Ingår i: SciPost Physics. - : Stichting SciPost. - 2542-4653. ; 14:4
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Tidskriftsartikel (refereegranskat)abstract
- Real-world topological semimetals typically exhibit Dirac and Weyl nodes that coexist with trivial Fermi pockets. This tends to mask the physics of the relativistic quasiparti-cles. Using the example of ZrTe5, we show that strain provides a powerful tool for in-situ tuning of the band structure such that all trivial pockets are pushed far away from the Fermi energy, but only for a certain range of Van der Waals gaps. Our results naturally reconcile contradicting reports on the presence or absence of additional pockets in ZrTe5, and provide a clear map of where to find a pure three-dimensional Dirac semimetallic phase in the structural parameter space of the material.
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