| 1. |
- Beal, Jacob, et al.
(author)
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Robust estimation of bacterial cell count from optical density
- 2020
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In: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Journal article (peer-reviewed)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. |
- Kristanl, Matej, et al.
(author)
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The Seventh Visual Object Tracking VOT2019 Challenge Results
- 2019
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In: 2019 IEEE/CVF INTERNATIONAL CONFERENCE ON COMPUTER VISION WORKSHOPS (ICCVW). - : IEEE COMPUTER SOC. - 9781728150239 ; , s. 2206-2241
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Conference paper (peer-reviewed)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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| 3. |
- Kristan, Matej, et al.
(author)
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The Visual Object Tracking VOT2017 challenge results
- 2017
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In: 2017 IEEE INTERNATIONAL CONFERENCE ON COMPUTER VISION WORKSHOPS (ICCVW 2017). - : IEEE. - 9781538610343 ; , s. 1949-1972
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Conference paper (peer-reviewed)abstract
- The Visual Object Tracking challenge VOT2017 is the fifth annual tracker benchmarking activity organized by the VOT initiative. Results of 51 trackers are presented; many are state-of-the-art published at major computer vision conferences or journals in recent years. The evaluation included the standard VOT and other popular methodologies and a new "real-time" experiment simulating a situation where a tracker processes images as if provided by a continuously running sensor. 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 VOT2017 goes beyond its predecessors by (i) improving the VOT public dataset and introducing a separate VOT2017 sequestered dataset, (ii) introducing a realtime tracking experiment and (iii) releasing a redesigned toolkit that supports complex experiments. The dataset, the evaluation kit and the results are publicly available at the challenge website(1).
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| 4. |
- Wei, Ting, et al.
(author)
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Developed and developing world responsibilities for historical climate change and CO2 mitigation
- 2012
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In: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 109:32, s. 12911-12915
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Journal article (peer-reviewed)abstract
- At the United Nations Framework Convention on Climate Change Conference in Cancun, in November 2010, the Heads of State reached an agreement on the aim of limiting the global temperature rise to 2 degrees C relative to preindustrial levels. They recognized that long-term future warming is primarily constrained by cumulative anthropogenic greenhouse gas emissions, that deep cuts in global emissions are required, and that action based on equity must be taken to meet this objective. However, negotiations on emission reduction among countries are increasingly fraught with difficulty, partly because of arguments about the responsibility for the ongoing temperature rise. Simulations with two earth-system models (NCAR/CESM and BNU-ESM) demonstrate that developed countries had contributed about 60-80%, developing countries about 20-40%, to the global temperature rise, upper ocean warming, and sea-ice reduction by 2005. Enacting pledges made at Cancun with continuation to 2100 leads to a reduction in global temperature rise relative to business as usual with a 1/3-2/3 (CESM 33-67%, BNU-ESM 35-65%) contribution from developed and developing countries, respectively. To prevent a temperature rise by 2 degrees C or more in 2100, it is necessary to fill the gap with more ambitious mitigation efforts.
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| 5. |
- Chen, Zhipeng, et al.
(author)
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Design, Synthesis, and Structure-Activity Relationship of N-Aryl-N'-(thiophen-2-yl) thiourea Derivatives as Novel and Specific Human TLR1/2 Agonists for Potential Cancer Immunotherapy
- 2021
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In: Journal of Medicinal Chemistry. - Washington, DC : American Chemical Society (ACS). - 0022-2623 .- 1520-4804. ; 64:11, s. 7371-7389
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Journal article (peer-reviewed)abstract
- The previous virtual screening of ten million compounds yielded two novel nonlipopeptide-like chemotypes as TLR2 agonists. Herein, we present the chemical optimization of our initial hit, 1-phenyl-3-(thiophen-2-yl) urea, which resulted in the identification of SMU-C80 (EC50 = 31.02 ± 1.01 nM) as a TLR2-specific agonist with a 370-fold improvement in bioactivity. Mechanistic studies revealed that SMU-C80, through TLR1/2, recruits the adaptor protein MyD88 and triggers the NF-κB pathway to release cytokines such as TNF-α and IL-1β from human, but not murine, cells. To the best of our knowledge, it is the first species-specific TLR1/2 agonist reported until now. Moreover, SMU-C80 increased the percentage of T, B, and NK cells ex vivo and activated the immune cells, which suppressed cancer cell growth in vitro. In summary, we obtained a highly efficient and specific human TLR1/2 agonist that acts through the MyD88 and NF-κB pathway, facilitating cytokine release and the simultaneous activation of immune cells that in turn affects the apoptosis of cancer cells. © 2021 American Chemical Society
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| 6. |
- Gravgaard Askjær, Thomas, et al.
(author)
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Multi-centennial Holocene climate variability in proxy records and transient model simulations
- 2022
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In: Quaternary Science Reviews. - : Elsevier BV. - 0277-3791 .- 1873-457X. ; 296
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Journal article (peer-reviewed)abstract
- Variability on centennial to multi-centennial timescales is mentioned as a feature in reconstructions of the Holocene climate. As more long transient model simulations with complex climate models become available and efforts have been made to compile large proxy databases, there is now a unique opportunity to study multi-centennial variability with greater detail and a large amount of data than earlier. This paper presents a spectral analysis of transient Holocene simulations from 9 models and 120 proxy records to find the common signals related to oscillation periods and geographic dependencies and discuss the implications for the potential driving mechanisms. Multi-centennial variability is significant in most proxy records, with the dominant oscillation periods around 120–130 years and an average of 240 years. Spectra of model-based global mean temperature (GMT) agree well with proxy evidence with significant multi-centennial variability in all simulations with the dominant oscillation periods around 120–150 years. It indicates a comparatively good agreement between model and proxy data. A lack of latitudinal dependencies in terms of oscillation period is found in both the model and proxy data. However, all model simulations have the highest spectral density distributed over the Northern hemisphere high latitudes, which could indicate a particular variability sensitivity or potential driving mechanisms in this region. Five models also have differentiated forcings simulations with various combinations of forcing agents. Significant multi-centennial variability with oscillation periods between 100 and 200 years is found in all forcing scenarios, including those with only orbital forcing. The different forcings induce some variability in the system. Yet, none appear to be the predominant driver based on the spectral analysis. Solar irradiance has long been hypothesized to be a primary driver of multi-centennial variability. However, all the simulations without this forcing have shown significant multi-centennial variability. The results then indicate that internal mechanisms operate on multi-centennial timescales, and the North Atlantic-Arctic is a region of interest for this aspect.
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| 7. |
- Li, Pan, et al.
(author)
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Silver nano-needles : Focused optical field induced solution synthesis and application in remote-excitation nanofocusing SERS
- 2019
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In: Nanoscale. - : Royal Society of Chemistry (RSC). - 2040-3364 .- 2040-3372. ; 11:5, s. 2153-2161
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Journal article (peer-reviewed)abstract
- Tapered metallic nanostructures that harbor surface plasmons are highly interesting for nanophotonic applications because of their waveguiding and field-focusing properties. Here, we developed a focused optical field induced solution synthesis for unique crystallized silver nano-needles. Under the focused laser spot, inhomogeneous Ag monomer concentration is created, which triggers the uniaxial growth of silver nanostructures along the radial direction with decreasing rate, forming nano-needle structures. These nano-needles are several micrometers long, with diameter attenuating from hundreds to tens of nanometers, and terminated by a sharp apex only a few nanometers in diameter. Moreover, nano-needles with atomically smooth surfaces show excellent performance for plasmonic waveguiding and unique near-field compression abilities. This nano-needle structure can be used for effective remote-excitation detection/sensing. We also demonstrate the assembling and picking up of nano-needles, which indicate potential applications in intracellular endoscopy, high resolution scanning tips, on-chip nanophotonic devices, etc.
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| 8. |
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| 9. |
- Yang, Zhilin, et al.
(author)
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Surface enhanced Raman scattering of pyridine adsorbed on Au@Pd core/shell nanoparticles
- 2009
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In: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 130:23
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Journal article (peer-reviewed)abstract
- Surface enhanced Raman scattering (SERS) of pyridine adsorbed on Au@Pd core/shell nanoparticles has been investigated theoretically with quantum chemical method, generalized Mie theory and three-dimensional finite-difference time domain (3D-FDTD) method. We first studied the influence of the coated Pd on the electronic structure of Au nanoparticle, and compared the electronic structure of Au-20 cluster with that of Au10Pd10 (core/shell) cluster. Second, we studied SERS spectroscopy of pyridine on Au@Pd core/shell nanoparticles, which revealed the rate of static chemical enhancement and electromagnetic enhancement in the experimental reports. Third, the influence of the Pd shell thickness to the optical absorption of Au@Pd core/shell nanoparticles was investigated with generalized Mie theory. Fourth, we studied the influence of the shell thickness to the local electric field enhancement with 3D-FDTD method. The theoretical results reveal that the static chemical enhancement and electromagnetic enhancement are in the order of 10 and 10(3), respectively. These theoretical studies promote the deeper understanding of the electronic structure and optical absorption properties of Au@Pd, and the mechanisms for SERS of molecule adsorbed on Au@Pd.
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