| 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. |
- Kristan, Matej, et al.
(författare)
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The Sixth Visual Object Tracking VOT2018 Challenge Results
- 2019
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Ingår i: Computer Vision – ECCV 2018 Workshops. - Cham : Springer Publishing Company. - 9783030110086 - 9783030110093 ; , s. 3-53
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Konferensbidrag (refereegranskat)abstract
- The Visual Object Tracking challenge VOT2018 is the sixth annual tracker benchmarking activity organized by the VOT initiative. Results of over eighty 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 and a “real-time” experiment simulating a situation where a tracker processes images as if provided by a continuously running sensor. A long-term tracking subchallenge has been introduced to the set of standard VOT sub-challenges. The new subchallenge focuses on long-term tracking properties, namely coping with target disappearance and reappearance. A new dataset has been compiled and a performance evaluation methodology that focuses on long-term tracking capabilities has been adopted. The VOT toolkit has been updated to support both standard short-term and the new long-term tracking subchallenges. 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 (http://votchallenge.net).
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| 3. |
- Ablikim, M., et al.
(författare)
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Observation of the Semileptonic Decay D-0 -> a(0)(980)(-)e(+)nu(e) and Evidence for D+ -> a(0)(980)(0)e(+)nu(e)
- 2018
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Ingår i: Physical Review Letters. - : AMER PHYSICAL SOC. - 0031-9007 .- 1079-7114. ; 121:8
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Tidskriftsartikel (refereegranskat)abstract
- Using an e(+)e(-) collision data sample of 2.93 fb(-1) collected at a center-of-mass energy of 3.773 GeV by the BESIII detector at BEPCII, we report the observation of D-0 -> a(0)(980)(-)e(+)nu(e) and evidence for D+ -> a(0)(980)(0)e(+)nu(e) with significances of 6.4 sigma and 2.9 sigma, respectively. The absolute branching fractions are determined to be B(D-0 -> a(0)(980)(-)e(+)nu(e)) x B(a(0)(980)(-) -> eta pi(-)) = [1.33(-0.29)(+0.33)(stat) +/- 0.09(syst)] x 10(-4) and B(D+ -> a(0)(980)(0)e(+)nu(e)) x B(a(0)(980)(0) -> eta pi(0)) = [1.66(-0.66)(+0.81)(stat) +/- 0.11(syst) x 10(-4). This is the first time the a(0)(980) meson has been measured in a D-0 semileptonic decay, which would open one more interesting page in the investigation of the nature of the puzzling a(0)(980) states.
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| 4. |
- Attié, David, et al.
(författare)
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A time projection chamber with GEM-based readout
- 2017
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Ingår i: Nuclear Instruments and Methods in Physics Research, Section A: Accelerators, Spectrometers, Detectors and Associated Equipment. - : Elsevier BV. - 0168-9002. ; 856, s. 109-118
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Tidskriftsartikel (refereegranskat)abstract
- For the International Large Detector concept at the planned International Linear Collider, the use of time projection chambers (TPC) with micro-pattern gas detector readout as the main tracking detector is investigated. In this paper, results from a prototype TPC, placed in a 1. T solenoidal field and read out with three independent Gas Electron Multiplier (GEM) based readout modules, are reported. The TPC was exposed to a 6. GeV electron beam at the DESY II synchrotron. The efficiency for reconstructing hits, the measurement of the drift velocity, the space point resolution and the control of field inhomogeneities are presented.
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| 5. |
- Kristan, Matej, et al.
(författare)
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The Visual Object Tracking VOT2016 Challenge Results
- 2016
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Ingår i: COMPUTER VISION - ECCV 2016 WORKSHOPS, PT II. - Cham : SPRINGER INT PUBLISHING AG. - 9783319488813 - 9783319488806 ; , s. 777-823
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Konferensbidrag (refereegranskat)abstract
- The Visual Object Tracking challenge VOT2016 aims at comparing short-term single-object visual trackers that do not apply pre-learned models of object appearance. Results of 70 trackers are presented, with a large number of trackers being published at major computer vision conferences and journals in the recent years. The number of tested state-of-the-art trackers makes the VOT 2016 the largest and most challenging benchmark on short-term tracking to date. For each participating tracker, a short description is provided in the Appendix. The VOT2016 goes beyond its predecessors by (i) introducing a new semi-automatic ground truth bounding box annotation methodology and (ii) extending the evaluation system with the no-reset experiment.
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| 6. |
- Kristan, Matej, et al.
(författare)
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The Visual Object Tracking VOT2017 challenge results
- 2017
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Ingår i: 2017 IEEE INTERNATIONAL CONFERENCE ON COMPUTER VISION WORKSHOPS (ICCVW 2017). - : IEEE. - 9781538610343 ; , s. 1949-1972
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Konferensbidrag (refereegranskat)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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| 7. |
- Xu, Yongtao, et al.
(författare)
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Design Two Novel Tetrahydroquinoline Derivatives against Anticancer Target LSD1 with 3D-QSAR Model and Molecular Simulation
- 2022
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Ingår i: Molecules. - : MDPI AG. - 1420-3049. ; 27:23
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Tidskriftsartikel (refereegranskat)abstract
- Lysine-specific demethylase 1 (LSD1) is a histone-modifying enzyme, which is a significant target for anticancer drug research. In this work, 40 reported tetrahydroquinoline-derivative inhibitors targeting LSD1 were studied to establish the three-dimensional quantitative structure–activity relationship (3D-QSAR). The established models CoMFA (Comparative Molecular Field Analysis (q2 = 0.778, (Formula presented.) = 0.709)) and CoMSIA (Comparative Molecular Similarity Index Analysis (q2 = 0.764, (Formula presented.) = 0.713)) yielded good statistical and predictive properties. Based on the corresponding contour maps, seven novel tetrahydroquinoline derivatives were designed. For more information, three of the compounds (D1, D4, and Z17) and the template molecule 18x were explored with molecular dynamics simulations, binding free energy calculations by MM/PBSA method as well as the ADME (absorption, distribution, metabolism, and excretion) prediction. The results suggested that D1, D4, and Z17 performed better than template molecule 18x due to the introduction of the amino and hydrophobic groups, especially for the D1 and D4, which will provide guidance for the design of LSD1 inhibitors.
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| 8. |
- Yin, Shi, et al.
(författare)
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Experimental investigation of near-field stream-wise flow development and spatial structure in triple buoyant plumes
- 2019
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Ingår i: Building and Environment. - : Elsevier Ltd. - 0360-1323 .- 1873-684X. ; 149, s. 79-89
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Tidskriftsartikel (refereegranskat)abstract
- This paper presents a systematic experimental study on stream-wise flow development and spatial structure of triple buoyant plumes. Two-dimensional Particle Image Velocimetry (2-D PIV) is employed to resolve velocity fields. Stream-wise axial velocity profiles, flow structure, flow region parameters, and self-similarity properties are analyzed at different configurations that are characterized by spacing ratios S/W (source spacing S divided by source width W). From velocity fields and axial velocity profiles, a similar stream-wise developing trend is identified in different source configurations. When near-field plumes travel downstream, axial velocities increase rapidly, off-center velocity peaks get merged with the central peak, and the number of velocity peaks reduces with the downstream distance. A compact source layout, comparing with the wide one, could enhance the near-field plumes interaction and promote the plumes deflection significantly. Fundamentally, the stream-wise spatial structure of the triple plumes initially consists of a converging region, followed by a merging region, and finally a combined region. By examining the averaged velocity fields, flow recirculation with negative axial velocities is found to scarcely exist in the converging region. Merging level Zm and quasi-combined level Zqc are analyzed quantitatively and statistically. Within the studied S/W range, the normalized Zm shows a linear increase with S/W in the formula of Zm/H=2.007(S/W)+1.173 and the normalized Zqc gives a power law increase with S/W in the formula of Zqc/H=6.035(S/W)0.4959. In addition, triple plumes are found to establish self-similarity approximately at Z = 3H with S/W of 0.2 and at Z = 4.5H with S/W of 0.5.
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| 9. |
- Yin, Shi, et al.
(författare)
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Experimental study of thermal plumes generated by a cluster of high-rise compact buildings under moderate background wind conditions
- 2020
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Ingår i: Building and Environment. - : Elsevier. - 0360-1323 .- 1873-684X. ; 181
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Tidskriftsartikel (refereegranskat)abstract
- When background wind is moderate, urban environment may face great challenges as removal ability of airborne pollutants, anthropogenic heat and moisture reduces. Under this condition, buoyancy-driven flow can break the dominant role of the background wind and affect the urban environment greatly. Knowledge of buoyant flow dynamics is essential for understanding urban wind/thermal environment and related pollutant transport. As one important buoyant flow, thermal plumes generated by a cluster of high-rise compact buildings are modelled using a laboratory water channel in this study. Flow similarity, when the buoyancy is prominent, is well satisfied. Mean flows, turbulent statistics, and rising features under different Froude (Fr) numbers are systematically explored by two-dimensional particle image velocimetry (PIV) technique. Overall, the transition of buoyancy-dominated and wind-dominated flow dynamics is observed when Fr number varies. For horizontal and vertical velocity components, peak magnitude and position are quantitatively determined on four building poles. Fr number obviously changes the relative magnitude of v-peak among four poles. Turbulence statistics, including velocity variance, turbulence kinetic energy, power spectral density, turbulent momentum flux, and turbulence production, are systematically analyzed, which show consistent results. As Fr number decreases, the plume mixing is enhanced. When particularly aiming at the plume region, smaller Fr numbers usually make the maximum velocities occur more in the plume central part rather than the boundaries. A quantitative rational function is given to describe the relation between Fr number and the rising angle, as a = 8.76/(Frq + 0.097).
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| 10. |
- Yin, Shi, et al.
(författare)
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PIV based POD analysis of coherent structures in flow patterns generated by triple interacting buoyant plumes
- 2019
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Ingår i: Building and Environment. - : Elsevier BV. - 0360-1323 .- 1873-684X. ; 158, s. 165-181
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Tidskriftsartikel (refereegranskat)abstract
- The paper performs an investigation on multi-scale coherent structures that exist in different flow patterns of triple interacting plumes. Time-averaged and turbulent flow characteristics are first obtained by the two-dimensional (2-D) particle image velocimetry (PIV) technique. Proper orthogonal decomposition (POD) method is then applied to extract the dominant coherent structures. Energy contributions, POD modes, and POD coefficients are systematically explored to understand the spatial-temporal characteristics of the coherent structures. The first three POD modes are most important in the turbulent kinetic energy (TKE). Mode 1, as the most dominant mode, can contain about 10% TKE in an average sense. In addition, the first 12–14 POD modes can totally contribute 50% TKE. Hierarchical four-scale flow structures, independent of the flow patterns, are clearly identified when mode number increases, which are successively characterized by main flows (the 1st scale), larger-scale outer-side vortex rings (the 2nd scale), shear-layer vortex shedding (the 3rd scale), and smaller-scale homogeneous turbulent vortices (the 4th scale). Frequency spectra analysis confirms the co-existence of lower-frequency and higher-frequency periodic cycles in one certain POD mode. Dominant frequencies of the first three POD coefficient series (a1–a3) fall into the range of 0.025–0.187 Hz. Probability density analysis has identified negative/positive peak probability densities of the series a1. Cumulative probabilities of negative and positive coefficients are approximately equivalent during the sampling period.
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| 11. |
- Yin, Shi, et al.
(författare)
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Unsteady large-scale flow patterns and dynamic vortex movement in near-field triple buoyant plumes
- 2018
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Ingår i: Building and Environment. - : Elsevier Ltd. - 0360-1323 .- 1873-684X. ; 142, s. 288-300
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Tidskriftsartikel (refereegranskat)abstract
- Unsteady flow patterns of interacting buoyant plumes are important for buoyant ventilation and particularly influence pollutant and heat transports in indoor and outdoor environments. This study reveals fundamental large-scale flow patterns in triple building plumes, investigates vortex moving trends during the pattern transition processes, and explores possible mechanisms of pattern diversity by two-dimensional (2-D) Particle Image Velocimetry (PIV). Total five tests are studied, including three different heat strengths Q (180, 90, and 30 W) and three source layouts characterized by the ratios of source spacing S to source width W (0.2, 0.5, and 1.0). Streamline distributions and axial velocity profiles clearly reveal three fundamental global flow patterns: a right-slanting asymmetrical flow pattern, a left-slanting asymmetrical flow pattern, and an axisymmetric flow pattern. Correspondingly, it indicates four basic transition processes, i.e., right-to-center, left-to-center, center-to-right, and center-to-left transitions (“center” represents the axisymmetric pattern). A novel vortex tracking method, based on lambda-2 (λ2) criterion and principles of the PIV technique, is developed and successfully applied to qualitatively track the vortex moving trends during the transition processes. The regular vortex moving trends are found to be reasonably consistent with the global pattern transition trends. The flow pattern diversity is speculated to be mainly driven by unstable heat source wall flows and downstream swaying motions in this study. These critical unstable motions are considered to probably relate to unstable lateral entrainment and vortex interaction, particularly beside the central plume. Consistently, the regular vortex moving trends are usually observed in and around the central plume.
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| 12. |
- Zhao, Xiaoyu, et al.
(författare)
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Identification of genetically predicted DNA methylation markers associated with non–small cell lung cancer risk among 34,964 cases and 448,579 controls
- 2024
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Ingår i: Cancer. - : John Wiley & Sons. - 0008-543X .- 1097-0142. ; 130:6, s. 913-926
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Tidskriftsartikel (refereegranskat)abstract
- Background: Although the associations between genetic variations and lung cancer risk have been explored, the epigenetic consequences of DNA methylation in lung cancer development are largely unknown. Here, the genetically predicted DNA methylation markers associated with non–small cell lung cancer (NSCLC) risk by a two-stage case-control design were investigated.Methods: The genetic prediction models for methylation levels based on genetic and methylation data of 1595 subjects from the Framingham Heart Study were established. The prediction models were applied to a fixed-effect meta-analysis of screening data sets with 27,120 NSCLC cases and 27,355 controls to identify the methylation markers, which were then replicated in independent data sets with 7844 lung cancer cases and 421,224 controls. Also performed was a multi-omics functional annotation for the identified CpGs by integrating genomics, epigenomics, and transcriptomics and investigation of the potential regulation pathways.Results: Of the 29,894 CpG sites passing the quality control, 39 CpGs associated with NSCLC risk (Bonferroni-corrected p ≤ 1.67 × 10−6) were originally identified. Of these, 16 CpGs remained significant in the validation stage (Bonferroni-corrected p ≤ 1.28 × 10−3), including four novel CpGs. Multi-omics functional annotation showed nine of 16 CpGs were potentially functional biomarkers for NSCLC risk. Thirty-five genes within a 1-Mb window of 12 CpGs that might be involved in regulatory pathways of NSCLC risk were identified.Conclusions: Sixteen promising DNA methylation markers associated with NSCLC were identified. Changes of the methylation level at these CpGs might influence the development of NSCLC by regulating the expression of genes nearby.Plain Language Summary: The epigenetic consequences of DNA methylation in lung cancer development are still largely unknown. This study used summary data of large-scale genome-wide association studies to investigate the associations between genetically predicted levels of methylation biomarkers and non–small cell lung cancer risk at the first time. This study looked at how well larotrectinib worked in adult patients with sarcomas caused by TRK fusion proteins. These findings will provide a unique insight into the epigenetic susceptibility mechanisms of lung cancer.
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