| 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. |
- Deng, Bin, et al.
(author)
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Ketamine inhibits TNF-α-induced cecal damage by enhancing RIP1 ubiquitination to attenuate lethal SIRS
- 2022
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In: Cell death discovery. - : Springer Science and Business Media LLC. - 2058-7716. ; 8:1
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Journal article (peer-reviewed)abstract
- Systemic inflammatory response syndrome (SIRS) is a sepsis-associated inflammatory state and a self-defense mechanism against specific and nonspecific stimuli. Ketamine influences many key processes that are altered during sepsis. However, the underlying mechanisms remain incompletely understood. In this study, TNF-α-treated mice, as well as HT-29 and L929 cell models, were applied to characterize TNF-α-induced systemic and local cecal tissue inflammatory responses. Behavioral, biochemical, histological, and molecular biological approaches were applied to illustrate the related processes. Mice with TNF-α-induced SIRS showed systemic and local cecal tissue inflammatory responses, as indicated by increased levels of high mobility group box 1 protein (HMGB1), chemokines (C-X-C motif) ligand 10 (CXCL10), interleukin-6 (IL-6), and IL-10, as well as high mortality. Ketamine pretreatment alleviated death rates, symptoms, and the production of inflammatory cytokines induced by TNF-α in mice. Moreover, ketamine also protected the mice from TNF-α-induced cecal damage by suppressing the phosphorylation of receptor-interacting serine/threonine-protein kinase 3 (RIP3) and mixed lineage kinase domain-like protein (MLKL). In addition, our results showed that ketamine efficiently inhibited TNF-α-induced necroptosis in HT-29 and L929 cells. Furthermore, we explored the mechanism using different L929 cell lines. The results displayed that ketamine inhibited TNF-α-induced necroptosis by enhancing RIP1 ubiquitination and reducing the RIP1-RIP3 and RIP3-MLKL interactions, as well as the formation of necrosomes. Thus, our study may provide a new theoretical and experimental basis for treating diseases characterized by SIRS-associated inflammatory factor storms. Moreover, our exploration may provide potential molecular mechanisms and targets for therapeutic intervention and clinical application of ketamine.
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| 3. |
- Dong, Shuo, et al.
(author)
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Direct measurement of key exciton properties: Energy, dynamics, and spatial distribution of the wave function
- 2021
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In: Natural Sciences. - : Wiley. - 2698-6248. ; 1:1
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Journal article (peer-reviewed)abstract
- Excitons, Coulomb-bound electron–hole pairs, are the fundamental excitations governing the optoelectronic properties of semiconductors. Although optical signatures of excitons have been studied extensively, experimental access to the excitonic wave function itself has been elusive. Using multidimensional photoemission spectroscopy, we present a momentum-, energy-, and time-resolved perspective on excitons in the layered semiconductor WSe2. By tuning the excitation wavelength, we determine the energy–momentum signature of bright exciton formation and its difference from conventional single-particle excited states. The multidimensional data allow to retrieve fundamental exciton properties like the binding energy and the exciton–lattice coupling and to reconstruct the real-space excitonic distribution function via Fourier transform. All quantities are in excellent agreement with microscopic calculations. Our approach provides a full characterization of the exciton properties and is applicable to bright and dark excitons in semiconducting materials, heterostructures, and devices. Key points: The full life cycle of excitons is recorded with time- and angle-resolved photoemission spectroscopy. The real-space distribution of the excitonic wave function is visualized. Direct measurement of the exciton-phonon interaction.
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| 4. |
- Kristan, Matej, et al.
(author)
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The first visual object tracking segmentation VOTS2023 challenge results
- 2023
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In: 2023 IEEE/CVF International conference on computer vision workshops (ICCVW). - : Institute of Electrical and Electronics Engineers Inc.. - 9798350307443 - 9798350307450 ; , s. 1788-1810
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Conference paper (peer-reviewed)abstract
- The Visual Object Tracking Segmentation VOTS2023 challenge is the eleventh annual tracker benchmarking activity of the VOT initiative. This challenge is the first to merge short-term and long-term as well as single-target and multiple-target tracking with segmentation masks as the only target location specification. A new dataset was created; the ground truth has been withheld to prevent overfitting. New performance measures and evaluation protocols have been created along with a new toolkit and an evaluation server. Results of the presented 47 trackers indicate that modern tracking frameworks are well-suited to deal with convergence of short-term and long-term tracking and that multiple and single target tracking can be considered a single problem. A leaderboard, with participating trackers details, the source code, the datasets, and the evaluation kit are publicly available at the challenge website1
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| 5. |
- Scheuner, Joel, 1991, et al.
(author)
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CrossFit: Fine-grained Benchmarking of Serverless Application Performance across Cloud Providers
- 2022
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In: Proceedings - 2022 IEEE/ACM 15th International Conference on Utility and Cloud Computing, UCC 2022. ; , s. 51-60
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Conference paper (peer-reviewed)abstract
- Serverless computing emerged as a promising cloud computing paradigm for deploying cloud-native applications but raises new performance challenges. Existing performance evaluation studies focus on micro-benchmarking to measure an individual aspect of serverless functions, such as CPU speed, but lack an in-depth analysis of differences in application performance across cloud providers. This paper presents CrossFit, an approach for detailed and fair cross-provider performance benchmarking of serverless applications based on a providerindependent tracing model. Our case study demonstrates how detailed distributed tracing enables drill-down analysis to explain performance differences between two leading cloud providers, AWS and Azure. The results for an asynchronous application show that trigger time contributes most delay to the end-to-end latency and explains the main performance difference between cloud providers. Our results further reveal how increasing and bursty workloads affect performance stability, median latency, and tail latency.
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| 6. |
- Zhang, Bin, et al.
(author)
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Single-Cell RNA-Seq Analysis Reveals Macrophages Are Involved in the Pathogenesis of Human Sporadic Acute Type A Aortic Dissection
- 2023
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In: Biomolecules. - : MDPI. - 2218-273X. ; 13:2
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Journal article (peer-reviewed)abstract
- Macrophages play an important role in the progression of sporadic acute type A aortic dissection (ATAAD). The aim of this study was to characterize the cellular heterogeneity of macrophages in ATAAD tissues by scRNA-seq. Ascending aortic wall tissue from six ATAAD patients and three heart transplant donors was assessed by scRNA-seq and then analyzed and validated by various bioinformatic algorithms and histopathology experiments. The results revealed that the proportion of macrophages in ATAAD tissues (24.51%) was significantly higher than that in normal tissues (13.69%). Among the six macrophage subclusters, pro-inflammatory macrophages accounted for 14.96% of macrophages in the AD group and 0.18% in the normal group. Chemokine- and inflammation-related genes (CCL2, CCL20, S100A8, and S100A9) were expressed more intensively in macrophages in ATAAD tissue than in those in normal tissue. Additionally, intercellular communication analysis and transcription factor analysis indicated the activation of inflammation and degradation of the extracellular matrix in ATAAD tissue. Finally, immunohistochemistry, immunofluorescence, and Western blot experiments confirmed the overexpression of macrophage marker genes (CD68 and CD163) and matrix metalloproteinases (MMP9 and MMP2) in ATAAD tissue. Collectively, our study provides a preliminary evaluation of the role of macrophages in ATAAD, and the results could aid in the development of therapeutic options in the future.
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