| 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. |
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| 3. |
- Kristanl, Matej, et al.
(författare)
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The Seventh Visual Object Tracking VOT2019 Challenge Results
- 2019
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Ingår i: 2019 IEEE/CVF INTERNATIONAL CONFERENCE ON COMPUTER VISION WORKSHOPS (ICCVW). - : IEEE COMPUTER SOC. - 9781728150239 ; , s. 2206-2241
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Konferensbidrag (refereegranskat)abstract
- The Visual Object Tracking challenge VOT2019 is the seventh annual tracker benchmarking activity organized by the VOT initiative. Results of 81 trackers are presented; many are state-of-the-art trackers published at major computer vision conferences or in journals in the recent years. The evaluation included the standard VOT and other popular methodologies for short-term tracking analysis as well as the standard VOT methodology for long-term tracking analysis. The VOT2019 challenge was composed of five challenges focusing on different tracking domains: (i) VOT-ST2019 challenge focused on short-term tracking in RGB, (ii) VOT-RT2019 challenge focused on "real-time" short-term tracking in RGB, (iii) VOT-LT2019 focused on long-term tracking namely coping with target disappearance and reappearance. Two new challenges have been introduced: (iv) VOT-RGBT2019 challenge focused on short-term tracking in RGB and thermal imagery and (v) VOT-RGBD2019 challenge focused on long-term tracking in RGB and depth imagery. The VOT-ST2019, VOT-RT2019 and VOT-LT2019 datasets were refreshed while new datasets were introduced for VOT-RGBT2019 and VOT-RGBD2019. The VOT toolkit has been updated to support both standard short-term, long-term tracking and tracking with multi-channel imagery. Performance of the tested trackers typically by far exceeds standard baselines. The source code for most of the trackers is publicly available from the VOT page. The dataset, the evaluation kit and the results are publicly available at the challenge website(1).
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| 4. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 5. |
- Ching, Tao-Chung, et al.
(författare)
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The JCMT BISTRO-2 Survey: Magnetic Fields of the Massive DR21 Filament
- 2022
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Ingår i: Astrophysical Journal. - : American Astronomical Society. - 1538-4357 .- 0004-637X. ; 941:2
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Tidskriftsartikel (refereegranskat)abstract
- We present 850 mu m dust polarization observations of the massive DR21 filament from the B-fields In STar-forming Region Observations (BISTRO) survey, using the POL-2 polarimeter and the SCUBA-2 camera on the James Clerk Maxwell Telescope. We detect ordered magnetic fields perpendicular to the parsec-scale ridge of the DR21 main filament. In the subfilaments, the magnetic fields are mainly parallel to the filamentary structures and smoothly connect to the magnetic fields of the main filament. We compare the POL-2 and Planck dust polarization observations to study the magnetic field structures of the DR21 filament on 0.1-10 pc scales. The magnetic fields revealed in the Planck data are well-aligned with those of the POL-2 data, indicating a smooth variation of magnetic fields from large to small scales. The plane-of-sky magnetic field strengths derived from angular dispersion functions of dust polarization are 0.6-1.0 mG in the DR21 filament and similar to 0.1 mG in the surrounding ambient gas. The mass-to-flux ratios are found to be magnetically supercritical in the filament and slightly subcritical to nearly critical in the ambient gas. The alignment between column density structures and magnetic fields changes from random alignment in the low-density ambient gas probed by Planck to mostly perpendicular in the high-density main filament probed by James Clerk Maxwell Telescope. The magnetic field structures of the DR21 filament are in agreement with MHD simulations of a strongly magnetized medium, suggesting that magnetic fields play an important role in shaping the DR21 main filament and subfilaments.
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| 6. |
- Tang, Ting-Ting, et al.
(författare)
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Impaired thymic export and apoptosis contribute to regulatory T-cell defects in patients with chronic heart failure.
- 2011
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Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203 .- 1932-6203. ; 6:9, s. e24272-
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Tidskriftsartikel (refereegranskat)abstract
- Animal studies suggest that regulatory T (T(reg)) cells play a beneficial role in ventricular remodeling and our previous data have demonstrated defects of T(reg) cells in patients with chronic heart failure (CHF). However, the mechanisms behind T(reg-)cell defects remained unknown. We here sought to elucidate the mechanism of T(reg-)cell defects in CHF patients.
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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. |
- Lubel, Emma, et al.
(författare)
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Accurate identification of motoneuron discharges from ultrasound images across the full muscle cross-section
- 2024
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Ingår i: IEEE Transactions on Biomedical Engineering. - : IEEE. - 0018-9294 .- 1558-2531. ; 71:5, s. 1466-1477
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Tidskriftsartikel (refereegranskat)abstract
- Objective: Non-invasive identification of motoneuron (MN) activity commonly uses electromyography (EMG). However, surface EMG (sEMG) detects only superficial sources, at less than approximately 10-mm depth. Intramuscular EMG can detect deep sources, but it is limited to sources within a few mm of the detection site. Conversely, ultrasound (US) images have high spatial resolution across the whole muscle cross-section. The activity of MNs can be extracted from US images due to the movements that MN activation generates in the innervated muscle fibers. Current US-based decomposition methods can accurately identify the location and average twitch induced by MN activity. However, they cannot accurately detect MN discharge times.Methods: Here, we present a method based on the convolutive blind source separation of US images to estimate MN discharge times with high accuracy. The method was validated across 10 participants using concomitant sEMG decomposition as the ground truth.Results: 140 unique MN spike trains were identified from US images, with a rate of agreement (RoA) with sEMG decomposition of 87.4 ± 10.3%. Over 50% of these MN spike trains had a RoA greater than 90%. Furthermore, with US, we identified additional MUs well beyond the sEMG detection volume, at up to >30 mm below the skin.Conclusion: The proposed method can identify discharges of MNs innervating muscle fibers in a large range of depths within the muscle from US images. Significance: The proposed methodology can non-invasively interface with the outer layers of the central nervous system innervating muscles across the full cross-section.
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| 9. |
- Lubel, Emma, et al.
(författare)
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Non-linearity in motor unit velocity twitch dynamics: Implications for ultrafast ultrasound source separation
- 2023
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Ingår i: IEEE transactions on neural systems and rehabilitation engineering. - : Institute of Electrical and Electronics Engineers (IEEE). - 1534-4320 .- 1558-0210.
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Tidskriftsartikel (refereegranskat)abstract
- Ultrasound (US) muscle image series can be used for peripheral human-machine interfacing based on global features, or even on the decomposition of US images into the contributions of individual motor units (MUs). With respect to state-of-the-art surface electromyography (sEMG), US provides higher spatial resolution and deeper penetration depth. However, the accuracy of current methods for direct US decomposition, even at low forces, is relatively poor. These methods are based on linear mathematical models of the contributions of MUs to US images. Here, we test the hypothesis of linearity by comparing the average velocity twitch profiles of MUs when varying the number of other concomitantly active units. We observe that the velocity twitch profile has a decreasing peak-to-peak amplitude when tracking the same target motor unit at progressively increasing contraction force levels, thus with an increasing number of concomitantly active units. This observation indicates non-linear factors in the generation model. Furthermore, we directly studied the impact of one MU on a neighboring MU, finding that the effect of one source on the other is not symmetrical and may be related to unit size. We conclude that a linear approximation is partly limiting the decomposition methods to decompose full velocity twitch trains from velocity images, highlighting the need for more advanced models and methods for US decomposition than those currently employed.
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| 10. |
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| 11. |
- Luo, Yang, et al.
(författare)
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Three-dimensional and temperature-dependent electronic structure of the heavy-fermion compound CePt2In7 studied by angle-resolved photoemission spectroscopy
- 2020
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Ingår i: Physical Review B. - : AMER PHYSICAL SOC. - 2469-9950 .- 2469-9969. ; 101:11
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Tidskriftsartikel (refereegranskat)abstract
- The three-dimensional and temperature-dependent electronic structures of the heavy-fermion superconductor CePt2In7 are investigated. Angle-resolved photoemission spectroscopy using variable photon energy establishes the existence of quasi-two- and three-dimensional Fermi surface topologies. Temperature-dependent 4d-4f on-resonance photoemission spectroscopies data reveal that heavy quasiparticle bands begin to form at a temperature well above the characteristic (coherence) temperature T+. The emergence of low-lying crystal electric field excitation may be responsible for the "relocalization" or the precursor to the establishment of heavy electrons coherence in heavy-fermion compounds. These findings provide critical insight into understanding the hybridization in heavy-fermion systems.
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| 12. |
- Tang, Weidong, et al.
(författare)
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The roles of metal oxidation states in perovskite semiconductors
- 2023
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Ingår i: Matter. - : CELL PRESS. - 2590-2393 .- 2590-2385. ; 6:11, s. 3782-3802
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Forskningsöversikt (refereegranskat)abstract
- Metal halide perovskites are an emerging materials platform for optoelectronic, spintronic, and thermoelectric applications. The field of perovskite materials and devices has progressed rapidly over the past decade. For halide perovskite materials, a range of physical and chemical properties such as crystal structure, bandgap, charge carrier density, and stability that govern the device functionalities are critically determined by the oxidation states of the B-site metal ions. However, such an important mechanistic connection unique to halide perovskites is not well established, limiting the pace of development in this area. In this review, we identify the roles of metal oxidation states in perovskite semiconductors. The redox reactions leading to these states, and their effects on the materials properties, are clarified. Finally, we suggest routes to improving device efficiency and stability from the perspective of oxidation state control.
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| 13. |
- Tang, Yu-xing, et al.
(författare)
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Determination of biomass-coal blending ratio by C-14 measurement in co-firing flue gas
- 2019
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Ingår i: Journal Of Zhejiang University-Science A. - 1673-565X. ; 20:7, s. 475-486
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Tidskriftsartikel (refereegranskat)abstract
- To verify the feasibility of using radiocarbon detection for the measurement of the biomass-coal blending ratio in co-firing heat and power plants, C-14 activity detection technology that uses benzene synthesis as the sample preparation method and a liquid scintillation counter as the detection instrument was studied. A benzene synthesis system was built to enrich carbon in the combustion flue gas in the form of benzene. The benzene sample was mixed with scintillator (butyl-PBD) and C-14 activity was measured using a liquid scintillation counter (Quantulus 1220). Three kinds of coal and six kinds of biomass were tested repeatedly. The measured C-14 activity was 0.3365 DPM/gC in Zhundong lignite, 0.2701 DPM/gC in Shenmu bitumite, and 0.3060 DPM/gC in Changzhi anthracite. These values were much higher than the instrument background activity. For the co-fired experiment, we used groups with biomass ratios (based on the carbon) of 6.51%, 12.95%, and 20.75%. A modified empirical expression to determine the biomass, coal blending ratio based on the C-14 activity measured in the co-firing flue gas, was proposed by analyzing and verifying measurement accuracy. From the C-14 measurements of the co-fired samples, the corresponding estimated biomass ratios were (5.540.48)%, (12.310.67)%, and (19.490.90)%. The absolute measurement error was around 1% for a typical biomass-coal co-firing application.
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