| 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. |
- Ebbestad, Jan Ove R., 1967-, et al.
(författare)
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Helcionelloid mollusks from the Lower Cambrian of Southern Sweden
- 2009
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Ingår i: Lundadagarna i Historisk Geologi och paleontology XI, 11-12 March, 2009, Abstracts with programme. ; , s. 7-
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- In 1879 Linnarsson described a diverse shelly fauna from the Exsulans Limestone at Kiviks Esperöd in Scania. A single ‘monoplacophoran’ mollusc was identified - Metoptoma barrandei - and Linnarsson noted that von Schmalensee had found a closely related form at Gislöf further to the south, albeit as fragmentary material. Reinvestigation of the locality at Gislövshammar by PC and JA has yielded close to 500 specimens of a diverse helcionelloid fauna. The material comes from a 40 cm interval of laminated siltstone with intercalated calcareous nodules in the Lower Cambrian Gislöv Formation (Holmia kjerulfi assemblage Zone). The specimens are mostly preserved as internal moulds but also impressions of the external surfaces are seen. A second, smaller collection from a loose block of more compact siltstone near Brantevik yielded two helcionelloid taxa of slightly different affinity to those from Gislövshammar. Altogether seven taxa can be recognized including Pelagiella, Marocella?, Latouchella?, Stenotheca? and two forms of Helcionella? The taxonomic identification of the various forms is preliminary at this stage. The only record of comparable or coeval helcionelloid molluscs from Scandinavia, beside that by Linnarsson (1879), is from the Tømten Member of the Ringsaker formation (Holmia kjerulfi assemblage Zone) in the Mjøsa district in Norway. Kiær (1918) recognised four taxa from this locality: two new species of Scenella and two species of Helcionella. The former he compared with Linnarsson’s form and with material from Newfoundland. Species of the latter genus were considered conspecific with North American material. In the Gislöv fauna only Marocella? enters into close comparison with Linnarsson’s and Kiær’s species, while the Helcionella species from the Brantevik block is most comparable to Kiær’s material. However, close comparison of the new Scanian material with material from eastern North American is pivotal to the taxonomic discussion at this stage. In particular, comparison with Avalonian faunas from south-eastern Newfoundland and New Brunswick described by C.D. Walcott and G.F. Matthews seem profitable. Within a wider scope, the new helcionelloid material opens up possibilities for improving both regional and intercontinental biostratigraphical correlation
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| 3. |
- Ahlberg, Per, et al.
(författare)
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Lotagnostus? : mystacinus, a rare agnostid from the Upper Cambrian of Sweden
- 2000
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Ingår i: Acta Palaeontologica Polonica. - 0567-7920. ; 45:1, s. 91-96
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Tidskriftsartikel (refereegranskat)abstract
- Agnostids afford the best means of correlating Cambrian strata, and they are widely used for intercontinental correlations. They are most common in open-marine deposits and reached a maximum diversity during the Middle and early Late Cambrian. About twenty species of agnostids are known from the Upper Cambrian of Scandinavia. Lotagnostus? mystacinus Tjernvik, 1953 is a rare agnostid from the Upper Cambrian Agnostus pisiformis Zone of south-central Sweden. It is redescribed following examination of the holotype and an additional pygidium. The outline and morphology of especially the pygidial posteroaxis, which is distinctly trilobate by a pair of deep notular furrows, suggest that the species is best classified as a species of Lotagnostus. If correctly assigned to Lotagnostus, it would be the oldest known species of that genus.
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| 4. |
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| 5. |
- Ahlgren, Sara, et al.
(författare)
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Targeting of HER2-expressing tumors with a site-specifically 99mTc-labeled recombinant affibody molecule, ZHER2:2395, with C-terminally engineered cysteine
- 2009
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Ingår i: Journal of Nuclear Medicine. - : Society of Nuclear Medicine. - 0161-5505 .- 1535-5667 .- 2159-662X. ; 50:5, s. 781-789
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Tidskriftsartikel (refereegranskat)abstract
- The detection of human epidermal growth factor receptor type 2 (HER2) expression in malignant tumors provides important information influencing patient management. Radionuclide in vivo imaging of HER2 may permit the detection of HER2 in both primary tumors and metastases by a single noninvasive procedure. Small (7 kDa) high-affinity anti-HER2 Affibody molecules may be suitable tracers for SPECT visualization of HER2-expressing tumors. The use of generator-produced (99m)Tc as a label would facilitate the prompt translation of anti-HER2 Affibody molecules into use in clinics. METHODS: A C-terminal cysteine was introduced into the Affibody molecule Z(HER2:342) to enable site-specific labeling with (99m)Tc. Two recombinant variants, His(6)-Z(HER2:342)-Cys (dissociation constant [K(D)], 29 pM) and Z(HER2:2395)-Cys, lacking a His tag (K(D), 27 pM), were labeled with (99m)Tc in yields exceeding 90%. The binding specificity and the cellular processing of Affibody molecules were studied in vitro. Biodistribution and gamma-camera imaging studies were performed in mice bearing HER2-expressing xenografts. RESULTS: (99m)Tc-His(6)-Z(HER2:342)-Cys was capable of targeting HER2-expressing SKOV-3 xenografts in SCID mice, but the liver radioactivity uptake was high. A series of comparative biodistribution experiments indicated that the presence of the His tag caused elevated accumulation in the liver. (99m)Tc-Z(HER2:2395)-Cys, not containing a His tag, showed low uptake in the liver and high and specific uptake in HER2-expressing xenografts. Four hours after injection, the radioactivity uptake values (percentage of injected activity per gram of tissue [%IA/g]) were 6.9 +/- 2.5 (mean +/- SD) %IA/g in LS174T xenografts (moderate level of HER2 expression) and 15 +/- 3 %IA/g in SKOV-3 xenografts (high level of HER2 expression). The corresponding tumor-to-blood ratios were 88 +/- 24 and 121 +/- 24, respectively. Both LS174T and SKOV-3 xenografts were clearly visualized with a clinical gamma-camera 1 h after injection of (99m)Tc-Z(HER2:2395)-Cys. CONCLUSION: The Affibody molecule (99m)Tc-Z(HER2:2395)-Cys is a promising tracer for SPECT visualization of HER2-expressing tumors.
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| 6. |
- Albinsson, John, et al.
(författare)
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A combination of parabolic and grid slope interpolation for 2D tissue displacement estimations
- 2017
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Ingår i: Medical & Biological Engineering & Computing. - : Springer Science and Business Media LLC. - 0140-0118 .- 1741-0444. ; 55:8, s. 1327-1338
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Tidskriftsartikel (refereegranskat)abstract
- Parabolic sub-sample interpolation for 2D block-matching motion estimation is computationally efficient. However, it is well known that the parabolic interpolation gives a biased motion estimate for displacements greater than |y.2| samples (y = 0, 1, …). Grid slope sub-sample interpolation is less biased, but it shows large variability for displacements close to y.0. We therefore propose to combine these sub-sample methods into one method (GS15PI) using a threshold to determine when to use which method. The proposed method was evaluated on simulated, phantom, and in vivo ultrasound cine loops and was compared to three sub-sample interpolation methods. On average, GS15PI reduced the absolute sub-sample estimation errors in the simulated and phantom cine loops by 14, 8, and 24% compared to sub-sample interpolation of the image, parabolic sub-sample interpolation, and grid slope sub-sample interpolation, respectively. The limited in vivo evaluation of estimations of the longitudinal movement of the common carotid artery using parabolic and grid slope sub-sample interpolation and GS15PI resulted in coefficient of variation (CV) values of 6.9, 7.5, and 6.8%, respectively. The proposed method is computationally efficient and has low bias and variance. The method is another step toward a fast and reliable method for clinical investigations of longitudinal movement of the arterial wall.
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| 7. |
- Albinsson, John, et al.
(författare)
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Combined use of Iteration, Quadratic Interpolation and an Extra Kernel for high-resolution 2D particle tracking : a first evaluation
- 2010
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Ingår i: 2010 ieee international ultrasonics symposium. - New York : IEEE Press. - 9781457703829 ; , s. 2000-2003
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Konferensbidrag (refereegranskat)abstract
- A novel 2D particle tracking method, that uses 1) iteration, 2) fast quadratic sub-pixel estimation (with only 28 multiplications per movement), and 3) a previous kernel, has been evaluated and compared with a full-search block-matching method. The comparison with high-frequency ultrasound data (40 MHz) was conducted in silico and on phantoms, which comprised lateral, diagonal, and ellipsoidal movement patterns with speeds of 0–15 mm/s. The mean tracking error was reduced by 68% in silico and 71% for the phantom measurements. When only sub-pixel estimation was used, the decrease in the tracking error was 61% in silico and 57% for the phantom measurements. As well as decreasing the tracking error, the new method only used 70% of the computational time needed by the full-search block-matching method. With a fast method having good tracking ability for high-frequency ultrasound data, we now have a tool to better investigate tissue movements and its dynamic functionality.
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| 8. |
- Albinsson, John, et al.
(författare)
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Improved tracking performance of lagrangian block-matching methodologies using block expansion in the time domain : In silico, phantom and invivo evaluations
- 2014
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Ingår i: Ultrasound in Medicine and Biology. - : Elsevier. - 0301-5629 .- 1879-291X. ; 40:10, s. 2508-2520
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Tidskriftsartikel (refereegranskat)abstract
- The aim of this study was to evaluate tracking performance when an extra reference block is added to a basic block-matching method, where the two reference blocks originate from two consecutive ultrasound frames. The use of an extra reference block was evaluated for two putative benefits: (i) an increase in tracking performance while maintaining the size of the reference blocks, evaluated using in silico and phantom cine loops; (ii) a reduction in the size of the reference blocks while maintaining the tracking performance, evaluated using in vivo cine loops of the common carotid artery where the longitudinal movement of the wall was estimated. The results indicated that tracking accuracy improved (mean - 48%, p<0.005 [in silico]; mean - 43%, p<0.01 [phantom]), and there was a reduction in size of the reference blocks while maintaining tracking performance (mean - 19%, p<0.01 [in vivo]). This novel method will facilitate further exploration of the longitudinal movement of the arterial wall. (C) 2014 World Federation for Ultrasound in Medicine & Biology.
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| 9. |
- Albinsson, John, et al.
(författare)
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Iterative 2D tissue motion tracking in ultrafast ultrasound imaging
- 2018
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Ingår i: Applied Sciences (Switzerland). - : MDPI AG. - 2076-3417. ; 8:5
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Tidskriftsartikel (refereegranskat)abstract
- In order to study longitudinal movement and intramural shearing of the arterial wall with a Lagrangian viewpoint using ultrafast ultrasound imaging, a new tracking scheme is required. We propose the use of an iterative tracking scheme based on temporary down-sampling of the frame-rate, anteroposterior tracking, and unbiased block-matching using two kernels per position estimate. The tracking scheme was evaluated on phantom B-mode cine loops and considered both velocity and displacement for a range of down-sampling factors (k = 1-128) at the start of the iterations. The cine loops had a frame rate of 1300-1500 Hz and were beamformed using delay-and-sum. The evaluation on phantom showed that both the mean estimation errors and the standard deviations decreased with an increasing initial down-sampling factor, while they increased with an increased velocity or larger pitch. A limited in vivo study shows that the major pattern of movement corresponds well with state-of-the-art low frame rate motion estimates, indicating that the proposed tracking scheme could enable the study of longitudinal movement of the intima-media complex using ultrafast ultrasound imaging, and is one step towards estimating the propagation velocity of the longitudinal movement of the arterial wall.
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| 10. |
- Bombarda, F., et al.
(författare)
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Runaway electron beam control
- 2019
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Ingår i: Plasma Physics and Controlled Fusion. - : IOP Publishing. - 1361-6587 .- 0741-3335. ; 61:1
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Tidskriftsartikel (refereegranskat)
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