| 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. |
- Kristan, Matej, et al.
(author)
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The Ninth Visual Object Tracking VOT2021 Challenge Results
- 2021
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In: 2021 IEEE/CVF INTERNATIONAL CONFERENCE ON COMPUTER VISION WORKSHOPS (ICCVW 2021). - : IEEE COMPUTER SOC. - 9781665401913 ; , s. 2711-2738
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Conference paper (peer-reviewed)abstract
- The Visual Object Tracking challenge VOT2021 is the ninth annual tracker benchmarking activity organized by the VOT initiative. Results of 71 trackers are presented; many are state-of-the-art trackers published at major computer vision conferences or in journals in recent years. The VOT2021 challenge was composed of four sub-challenges focusing on different tracking domains: (i) VOT-ST2021 challenge focused on short-term tracking in RGB, (ii) VOT-RT2021 challenge focused on "real-time" short-term tracking in RGB, (iii) VOT-LT2021 focused on long-term tracking, namely coping with target disappearance and reappearance and (iv) VOT-RGBD2021 challenge focused on long-term tracking in RGB and depth imagery. The VOT-ST2021 dataset was refreshed, while VOT-RGBD2021 introduces a training dataset and sequestered dataset for winner identification. The source code for most of the trackers, the datasets, the evaluation kit and the results along with the source code for most trackers are publicly available at the challenge website(1).
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| 3. |
- Abelev, Betty, et al.
(author)
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Long-range angular correlations on the near and away side in p-Pb collisions at root S-NN=5.02 TeV
- 2013
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In: Physics Letters. Section B: Nuclear, Elementary Particle and High-Energy Physics. - : Elsevier BV. - 0370-2693. ; 719:1-3, s. 29-41
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Journal article (peer-reviewed)abstract
- Angular correlations between charged trigger and associated particles are measured by the ALICE detector in p-Pb collisions at a nucleon-nucleon centre-of-mass energy of 5.02 TeV for transverse momentum ranges within 0.5 < P-T,P-assoc < P-T,P-trig < 4 GeV/c. The correlations are measured over two units of pseudorapidity and full azimuthal angle in different intervals of event multiplicity, and expressed as associated yield per trigger particle. Two long-range ridge-like structures, one on the near side and one on the away side, are observed when the per-trigger yield obtained in low-multiplicity events is subtracted from the one in high-multiplicity events. The excess on the near-side is qualitatively similar to that recently reported by the CMS Collaboration, while the excess on the away-side is reported for the first time. The two-ridge structure projected onto azimuthal angle is quantified with the second and third Fourier coefficients as well as by near-side and away-side yields and widths. The yields on the near side and on the away side are equal within the uncertainties for all studied event multiplicity and p(T) bins, and the widths show no significant evolution with event multiplicity or p(T). These findings suggest that the near-side ridge is accompanied by an essentially identical away-side ridge. (c) 2013 CERN. Published by Elsevier B.V. All rights reserved.
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| 4. |
- Abelev, Betty, et al.
(author)
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Measurement of prompt J/psi and beauty hadron production cross sections at mid-rapidity in pp collisions at root s=7 TeV
- 2012
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In: Journal of High Energy Physics. - 1029-8479. ; :11
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Journal article (peer-reviewed)abstract
- The ALICE experiment at the LHC has studied J/psi production at mid-rapidity in pp collisions at root s = 7 TeV through its electron pair decay on a data sample corresponding to an integrated luminosity L-int = 5.6 nb(-1). The fraction of J/psi from the decay of long-lived beauty hadrons was determined for J/psi candidates with transverse momentum p(t) > 1,3 GeV/c and rapidity vertical bar y vertical bar < 0.9. The cross section for prompt J/psi mesons, i.e. directly produced J/psi and prompt decays of heavier charmonium states such as the psi(2S) and chi(c) resonances, is sigma(prompt J/psi) (p(t) > 1.3 GeV/c, vertical bar y vertical bar < 0.9) = 8.3 +/- 0.8(stat.) +/- 1.1 (syst.)(-1.4)(+1.5) (syst. pol.) mu b. The cross section for the production of b-hadrons decaying to J/psi with p(t) > 1.3 GeV/c and vertical bar y vertical bar < 0.9 is a sigma(J/psi <- hB) (p(t) > 1.3 GeV/c, vertical bar y vertical bar < 0.9) = 1.46 +/- 0.38 (stat.)(-0.32)(+0.26) (syst.) mu b. The results are compared to QCD model predictions. The shape of the p(t) and y distributions of b-quarks predicted by perturbative QCD model calculations are used to extrapolate the measured cross section to derive the b (b) over bar pair total cross section and d sigma/dy at mid-rapidity.
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| 5. |
- Li, Guoqiang, et al.
(author)
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A comprehensive dataset of luminescence chronologies and environmental proxy indices of loess-paleosol deposits across Asia
- 2024
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In: npj Climate and Atmospheric Science. - : Springer Nature. - 2397-3722. ; 7:1
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Journal article (peer-reviewed)abstract
- Loess-paleosol sequences have been used in Asia to study climate and environmental changes during the Quaternary. The scarcity of age control datasets and proxy indices analysis data for Asian loess has limited our understanding of loess depositional processes and the reconstruction of paleoclimatic changes from loess-paleosol records. In this study, we present a dataset that includes 1785 quartz optically stimulated luminescence ages and 1038 K-feldspar post-infrared infrared stimulated luminescence ages from 128 loess-paleosol sequences located in different regions of Asia. We generate 38 high-resolution age-depth models of loess records based on the provided datasets. We provide data on 12,365 grain size records, 14,964 magnetic susceptibility records, 2204 CaCO3 content records, and 3326 color reflection records. This dataset contains the most detailed and accurate chronologies and proxy index data for loess records in Asia yet published. It provides fundamental data for understanding the spatial-temporal variations in loess depositional processes and climatic changes across the continent during the mid-late Quaternary.
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| 6. |
- Dong, Qibing, et al.
(author)
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Regulating concentration of surface oxygen vacancies in Bi 2 MoO 6 /Bi-MOF for boosting photocatalytic ammonia synthesis
- 2024
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In: Journal of Catalysis. - 0021-9517 .- 1090-2694. ; 433
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Journal article (peer-reviewed)abstract
- Surface oxygen vacancies (OVs) engineering has been widely adopted as an effective strategy to enhance photocatalytic performance. At present, photocatalytic systems capable of precisely regulating surface OVs concentrations, which could help illuminate the effects of the surface OVs concentration on N2 fixation activity, are still scarce. Herein, bismuth-based metal organic framework (Bi-MOF) was loaded onto the surface of Bi2MoO6 (BMO) as an operable platform, and the OVs concentration in the Bi-MOF component of BMO/Bi-MOF could be regulated by reduction of bismuth ions therein. Experimental results confirm that optimum construction of OVs in the Bi-MOF promotes the photoelectrons transfer from BMO to Bi-MOF, facilitating the activation of N2 at OVs. Consequently, the optimized catalyst shows superior performance in NH3 production, which reaches 125.78 μmol h−1 g−1, 21.4 higher than that of BMO. This work underline the significance of regulating surface OVs concentration, providing inspiration for the development of efficient OVs-modified photocatalysts.
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| 7. |
- Huang, Hongyun, et al.
(author)
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Clinical Cell Therapy Guidelines for Neurorestoration (IANR/CANR 2017)
- 2018
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In: Cell Transplantation. - : SAGE Publications. - 0963-6897 .- 1555-3892. ; 27:2, s. 310-324
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Research review (peer-reviewed)abstract
- Cell therapy has been shown to be a key clinical therapeutic option for central nervous system diseases or damage. Standardization of clinical cell therapy procedures is an important task for professional associations devoted to cell therapy. The Chinese Branch of the International Association of Neurorestoratology (IANR) completed the first set of guidelines governing the clinical application of neurorestoration in 2011. The IANR and the Chinese Association of Neurorestoratology (CANR) collaborated to propose the current version "Clinical Cell Therapy Guidelines for Neurorestoration (IANR/CANR 2017)". The IANR council board members and CANR committee members approved this proposal on September 1, 2016, and recommend it to clinical practitioners of cellular therapy. These guidelines include items of cell type nomenclature, cell quality control, minimal suggested cell doses, patient-informed consent, indications for undergoing cell therapy, contraindications for undergoing cell therapy, documentation of procedure and therapy, safety evaluation, efficacy evaluation, policy of repeated treatments, do not charge patients for unproven therapies, basic principles of cell therapy, and publishing responsibility.
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| 8. |
- Liu, Shaohui, et al.
(author)
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Data-Driven Controlled Synthesis of Oriented Quasi-Spherical CsPbBr3 Perovskite Materials
- 2024
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In: Angewandte Chemie International Edition. - : WILEY-V C H VERLAG GMBH. - 1433-7851 .- 1521-3773. ; 63:14
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Journal article (peer-reviewed)abstract
- Controlled synthesis of lead-halide perovskite crystals is challenging yet attractive because of the pivotal role played by the crystal structure and growth conditions in regulating their properties. This study introduces data-driven strategies for the controlled synthesis of oriented quasi-spherical CsPbBr3, alongside an investigation into the synthesis mechanism. High-throughput rapid characterization of absorption spectra and color under ultraviolet illumination was conducted using 23 possible ligands for the synthesis of CsPbBr3 crystals. The links between the absorption spectra slope (difference in the absorbance at 400 nm and 450 nm divided by a wavelength interval of 50 nm) and crystal size were determined through statistical analysis of more than 100 related publications. Big data analysis and machine learning were employed to investigate a total of 688 absorption spectra and 652 color values, revealing correlations between synthesis parameters and properties. Ex situ characterization confirmed successful synthesis of oriented quasi-spherical CsPbBr3 perovskites using polyvinylpyrrolidone and Acacia. Density functional theory calculations highlighted strong adsorption of Acacia on the (110) facet of CsPbBr3. Optical properties of the oriented quasi-spherical perovskites prepared with these data-driven strategies were significantly improved. This study demonstrates that data-driven controlled synthesis facilitates morphology-controlled perovskites with excellent optical properties.
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| 9. |
- Maddali, Manoj V., et al.
(author)
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Validation and utility of ARDS subphenotypes identified by machine-learning models using clinical data : an observational, multicohort, retrospective analysis
- 2022
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In: The Lancet Respiratory Medicine. - 2213-2600. ; 10:4, s. 367-377
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Journal article (peer-reviewed)abstract
- Background: Two acute respiratory distress syndrome (ARDS) subphenotypes (hyperinflammatory and hypoinflammatory) with distinct clinical and biological features and differential treatment responses have been identified using latent class analysis (LCA) in seven individual cohorts. To facilitate bedside identification of subphenotypes, clinical classifier models using readily available clinical variables have been described in four randomised controlled trials. We aimed to assess the performance of these models in observational cohorts of ARDS. Methods: In this observational, multicohort, retrospective study, we validated two machine-learning clinical classifier models for assigning ARDS subphenotypes in two observational cohorts of patients with ARDS: Early Assessment of Renal and Lung Injury (EARLI; n=335) and Validating Acute Lung Injury Markers for Diagnosis (VALID; n=452), with LCA-derived subphenotypes as the gold standard. The primary model comprised only vital signs and laboratory variables, and the secondary model comprised all predictors in the primary model, with the addition of ventilatory variables and demographics. Model performance was assessed by calculating the area under the receiver operating characteristic curve (AUC) and calibration plots, and assigning subphenotypes using a probability cutoff value of 0·5 to determine sensitivity, specificity, and accuracy of the assignments. We also assessed the performance of the primary model in EARLI using data automatically extracted from an electronic health record (EHR; EHR-derived EARLI cohort). In Large Observational Study to Understand the Global Impact of Severe Acute Respiratory Failure (LUNG SAFE; n=2813), a multinational, observational ARDS cohort, we applied a custom classifier model (with fewer variables than the primary model) to determine the prognostic value of the subphenotypes and tested their interaction with the positive end-expiratory pressure (PEEP) strategy, with 90-day mortality as the dependent variable. Findings: The primary clinical classifier model had an area under receiver operating characteristic curve (AUC) of 0·92 (95% CI 0·90–0·95) in EARLI and 0·88 (0·84–0·91) in VALID. Performance of the primary model was similar when using exclusively EHR-derived predictors compared with manually curated predictors (AUC=0·88 [95% CI 0·81–0·94] vs 0·92 [0·88–0·97]). In LUNG SAFE, 90-day mortality was higher in patients assigned the hyperinflammatory subphenotype than in those with the hypoinflammatory phenotype (414 [57%] of 725 vs 694 [33%] of 2088; p<0·0001). There was a significant treatment interaction with PEEP strategy and ARDS subphenotype (p=0·041), with lower 90-day mortality in the high PEEP group of patients with the hyperinflammatory subphenotype (hyperinflammatory subphenotype: 169 [54%] of 313 patients in the high PEEP group vs 127 [62%] of 205 patients in the low PEEP group; hypoinflammatory subphenotype: 231 [34%] of 675 patients in the high PEEP group vs 233 [32%] of 734 patients in the low PEEP group). Interpretation: Classifier models using clinical variables alone can accurately assign ARDS subphenotypes in observational cohorts. Application of these models can provide valuable prognostic information and could inform management strategies for personalised treatment, including application of PEEP, once prospectively validated. Funding: US National Institutes of Health and European Society of Intensive Care Medicine.
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| 10. |
- Zhang, Dezhi, et al.
(author)
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Phylogenetic Conflict Between Species Tree and Maternally Inherited Gene Trees in a Clade of Emberiza Buntings (Aves: Emberizidae)
- 2023
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In: SYSTEMATIC BIOLOGY. - 1063-5157 .- 1076-836X.
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Journal article (peer-reviewed)abstract
- Different genomic regions may reflect conflicting phylogenetic topologies primarily due to incomplete lineage sorting and/or gene flow. Genomic data are necessary to reconstruct the true species tree and explore potential causes of phylogenetic conflict. Here, we investigate the phylogenetic relationships of 4 Emberiza species (Aves: Emberizidae) and discuss the potential causes of the observed mitochondrial non-monophyly of Emberiza godlewskii (Godlewski's bunting) using phylogenomic analyses based on whole genome resequencing data from 41 birds. Analyses based on both the whole mitochondrial genome and similar to 39 kilobases from the non-recombining W chromosome reveal sister relationships between each the northern and southern populations of E. godlewskii with E. cioides and E. cia, respectively. In contrast, the monophyly of E. godlewskii is reflected by the phylogenetic signal of autosomal and Z chromosomal sequence data as well as demographic inference analyses, which-in combination-support the following tree topology: ([{E. godlewskii, E. cia}, E. cioides], E. jankowskii). Using D-statistics, we detected multiple gene flow events among different lineages, indicating pervasive introgressive hybridization within this clade. Introgression from an unsampled lineage that is sister to E. cioides or introgression from an unsampled mitochondrial + W chromosomal lineage of E. cioides into northern E. godlewskii may explain the phylogenetic conflict between the species tree estimated from genome-wide data versus mtDNA/W tree topologies. These results underscore the importance of using genomic data for phylogenetic reconstruction and species delimitation.
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