| 1. |
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| 2. |
- 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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| 3. |
- Bai, Yang, et al.
(författare)
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Geometry design of tethered small-molecule acceptor enables highly stable and efficient polymer solar cells
- 2023
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Ingår i: Nature Communications. - : NATURE PORTFOLIO. - 2041-1723. ; 14:1
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Tidskriftsartikel (refereegranskat)abstract
- With the power conversion efficiency of binary polymer solar cells dramatically improved, the thermal stability of the small-molecule acceptors raised the main concerns on the device operating stability. Here, to address this issue, thiophene-dicarboxylate spacer tethered small-molecule acceptors are designed, and their molecular geometries are further regulated via the thiophene-core isomerism engineering, affording dimeric TDY-alpha with a 2, 5-substitution and TDY-beta with 3, 4-substitution on the core. It shows that TDY-alpha processes a higher glass transition temperature, better crystallinity relative to its individual small-molecule acceptor segment and isomeric counterpart of TDY-beta, and amore stablemorphology with the polymer donor. As a result, the TDY-alpha based device delivers a higher device efficiency of 18.1%, and most important, achieves an extrapolated lifetime of about 35000 hours that retaining 80% of their initial efficiency. Our result suggests that with proper geometry design, the tethered small-molecule acceptors can achieve both high device efficiency and operating stability.
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| 4. |
- Barucca, G., et al.
(författare)
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Study of excited Ξ baryons with the P¯ ANDA detector
- 2021
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Ingår i: European Physical Journal A. - : Springer Nature. - 1434-6001 .- 1434-601X. ; 57:4
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Tidskriftsartikel (refereegranskat)abstract
- The study of baryon excitation spectra provides insight into the inner structure of baryons. So far, most of the world-wide efforts have been directed towards N∗ and Δ spectroscopy. Nevertheless, the study of the double and triple strange baryon spectrum provides independent information to the N∗ and Δ spectra. The future antiproton experiment P¯ANDA will provide direct access to final states containing a Ξ¯ Ξ pair, for which production cross sections up to μb are expected in p¯p reactions. With a luminosity of L= 10 31 cm- 2 s- 1 in the first phase of the experiment, the expected cross sections correspond to a production rate of ∼106events/day. With a nearly 4 π detector acceptance, P¯ANDA will thus be a hyperon factory. In this study, reactions of the type p¯p → Ξ¯ +Ξ∗ - as well as p¯p → Ξ¯ ∗ +Ξ- with various decay modes are investigated. For the exclusive reconstruction of the signal events a full decay tree fit is used, resulting in reconstruction efficiencies between 3 and 5%. This allows high statistics data to be collected within a few weeks of data taking.
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| 5. |
- Barucca, G., et al.
(författare)
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The potential of Λ and Ξ- studies with PANDA at FAIR
- 2021
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Ingår i: European Physical Journal A. - : Springer Nature. - 1434-6001 .- 1434-601X. ; 57:4
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Tidskriftsartikel (refereegranskat)abstract
- The antiproton experiment PANDA at FAIR is designed to bring hadron physics to a new level in terms of scope, precision and accuracy. In this work, its unique capability for studies of hyperons is outlined. We discuss ground-state hyperons as diagnostic tools to study non-perturbative aspects of the strong interaction, and fundamental symmetries. New simulation studies have been carried out for two benchmark hyperon-antihyperon production channels: p¯ p→ Λ¯ Λ and p¯ p→ Ξ¯ +Ξ-. The results, presented in detail in this paper, show that hyperon-antihyperon pairs from these reactions can be exclusively reconstructed with high efficiency and very low background contamination. In addition, the polarisation and spin correlations have been studied, exploiting the weak, self-analysing decay of hyperons and antihyperons. Two independent approaches to the finite efficiency have been applied and evaluated: one standard multidimensional efficiency correction approach, and one efficiency independent approach. The applicability of the latter was thoroughly evaluated for all channels, beam momenta and observables. The standard method yields good results in all cases, and shows that spin observables can be studied with high precision and accuracy already in the first phase of data taking with PANDA.
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| 6. |
- Chang, Qi, et al.
(författare)
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DeepRecon : Joint 2D Cardiac Segmentation and 3D Volume Reconstruction via a Structure-Specific Generative Method
- 2022
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Ingår i: Medical Image Computing and Computer Assisted Intervention – MICCAI 2022 - 25th International Conference, Proceedings. - Cham : Springer Nature Switzerland. - 0302-9743 .- 1611-3349. - 9783031164392 ; 13434 LNCS, s. 567-577
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Konferensbidrag (refereegranskat)abstract
- Joint 2D cardiac segmentation and 3D volume reconstruction are fundamental in building statistical cardiac anatomy models and understanding functional mechanisms from motion patterns. However, due to the low through-plane resolution of cine MR and high inter-subject variance, accurately segmenting cardiac images and reconstructing the 3D volume are challenging. In this study, we propose an end-to-end latent-space-based framework, DeepRecon, that generates multiple clinically essential outcomes, including accurate image segmentation, synthetic high-resolution 3D image, and 3D reconstructed volume. Our method identifies the optimal latent representation of the cine image that contains accurate semantic information for cardiac structures. In particular, our model jointly generates synthetic images with accurate semantic information and segmentation of the cardiac structures using the optimal latent representation. We further explore downstream applications of 3D shape reconstruction and 4D motion pattern adaptation by the different latent-space manipulation strategies. The simultaneously generated high-resolution images present a high interpretable value to assess the cardiac shape and motion. Experimental results demonstrate the effectiveness of our approach on multiple fronts including 2D segmentation, 3D reconstruction, downstream 4D motion pattern adaption performance.
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| 7. |
- Feng, Shaohong, et al.
(författare)
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Dense sampling of bird diversity increases power of comparative genomics
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 587:7833
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Tidskriftsartikel (refereegranskat)abstract
- Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity(1-4). Sparse taxon sampling has previously been proposed to confound phylogenetic inference(5), and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species. A dataset of the genomes of 363 species from the Bird 10,000 Genomes Project shows increased power to detect shared and lineage-specific variation, demonstrating the importance of phylogenetically diverse taxon sampling in whole-genome sequencing.
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| 8. |
- Guo, J., et al.
(författare)
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Prenatal exposure to mixture of heavy metals, pesticides and phenols and IQ in children at 7 years of age : The SMBCS study
- 2020
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Ingår i: Environment International. - : Elsevier. - 0160-4120 .- 1873-6750. ; 139
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Tidskriftsartikel (refereegranskat)abstract
- Objective: Prenatal exposure to heavy metals, pesticides and phenols has been suggested to interfere with neurodevelopment, but the neurotoxicity of their mixtures is still unclear. We aimed to elucidate the associations of maternal urinary concentrations of selected chemical mixtures with intelligence quotient (IQ) in children.Methods: Maternal urinary concentrations of selected heavy metals, pesticide metabolites, and phenols were quantified in pregnant women who participated in the Sheyang Mini Birth Cohort Study (SMBCS) from June 2009 to January 2010. At age 7 years, child's IQ score was assessed using the Chinese version of Wechsler Intelligence Scale for Children (C-WISC) by trained pediatricians. Generalized linear regression models (GLM), Bayesian kernel machine regression (BKMR) models and elastic net regression (ENR) models were used to assess the associations of urinary concentrations individual chemicals and their mixtures with IQ scores of the 7-year-old children.Results: Of 326 mother-child pairs, single-chemical models indicated that prenatal urinary concentrations of lead (Pb) and bisphenol A (BPA) were significantly negatively associated with full intelligence quotient (FIQ) among children aged 7 years [β = −2.31, 95% confidence interval (CI): −4.13, −0.48; p = 0.013, sex interaction p-value = 0.076; β = −1.18, 95% CI: −2.21, −0.15; p = 0.025; sex interaction p-value = 0.296, for Pb and BPA, respectively]. Stratified analysis by sex indicated that the associations were only statistically significant in boys. In multi-chemical BKMR and ENR models, statistically significant inverse association was found between prenatal urinary Pb level and boy's FIQ scores at 7 years. Furthermore, BKMR analysis indicated that the overall mixture was associated with decreases in boy's IQ when all the chemicals’ concentrations were at their 75th percentiles or higher, compared to at their 50th percentiles. ENR models revealed that maternal urinary Pb levels were statistically significantly associated with lower FIQ scores (β = −2.20, 95% CI: −4.20, −0.20; p = 0.031).Conclusions: Prenatal exposure to selected chemical mixtures may affect intellectual performance at 7 years of age, particularly in boys. Pb and BPA were suspected as primary chemicals associated with child neurodevelopment.
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| 9. |
- Huang, Qi, et al.
(författare)
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A method for generating case-specific vehicle models from a single-view vehicle image for accurate pedestrian injury reconstructions
- 2024
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Ingår i: Accident Analysis and Prevention. - : Elsevier BV. - 0001-4575 .- 1879-2057. ; 200
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Tidskriftsartikel (refereegranskat)abstract
- Developing vehicle finite element (FE) models that match real accident-involved vehicles is challenging. This is related to the intricate variety of geometric features and components. The current study proposes a novel method to efficiently and accurately generate case-specific buck models for car-to-pedestrian simulations. To achieve this, we implemented the vehicle side-view images to detect the horizontal position and roundness of two wheels to rectify distortions and deviations and then extracted the mid-section profiles for comparative calculations against baseline vehicle models to obtain the transformation matrices. Based on the generic buck model which consists of six key components and corresponding matrices, the case-specific buck model was generated semi-automatically based on the transformation metrics. Utilizing this image-based method, a total of 12 vehicle models representing four vehicle categories including family car (FCR), Roadster (RDS), small Sport Utility Vehicle (SUV), and large SUV were generated for car-to-pedestrian collision FE simulations in this study. The pedestrian head trajectories, total contact forces, head injury criterion (HIC), and brain injury criterion (BrIC) were analyzed comparatively. We found that, even within the same vehicle category and initial conditions, the variation in wrap around distance (WAD) spans 84–165 mm, in HIC ranges from 98 to 336, and in BrIC fluctuates between 1.25 and 1.46. These findings highlight the significant influence of vehicle frontal shape and underscore the necessity of using case-specific vehicle models in crash simulations. The proposed method provides a new approach for further vehicle structure optimization aiming at reducing pedestrian head injury and increasing traffic safety.
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| 10. |
- Zhang, Jiming, et al.
(författare)
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Early-life carbamate exposure and intelligence quotient of seven-year-old children
- 2020
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Ingår i: Environment International. - : Elsevier. - 0160-4120 .- 1873-6750. ; 145
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Tidskriftsartikel (refereegranskat)abstract
- Background: Early-life carbamate exposure during developmental period has been linked with adverse health effects and attracted attention.Methods: Three hundred and three children at age of seven were included in the current study. Urinary carbofuranphenol concentrations were measured using gas chromatography-tandem mass spectrometry. Verbal, performance and full-scale intelligence quotients (IQ(V), IQ(P), and IQ(FS)) were assessed using Wechsler Intelligence Scale for Children-Chinese Revised. Generalized linear models were used to explore the associations between carbofuranphenol levels and IQs. Generalized estimating equations were used to explore long-term health effect and sensitive time window.Results: Carbofuranphenol was detected in 96.6% of the seven-year-old urinary samples, the geometric mean, median, and inter quartile range of the carbofuranphenol concentrations were 0.67 mu g/L, 0.30 mu g/L, and 0.09-3.72 mu g/L, respectively, which were similar with the level of three-year-old children from the SMBCS cohort. Seven-year-old carbofuranphenol level was negatively associated with IQP [beta = -0.044; 95% confidence interval (CI): -0.087, -0.001; p = 0.045]. Three-year-old carbofuranphenol level was negatively associated with IQP (beta =-0.100; 95% CI: -0.186, -0.014; p= 0.022) and IQFS (beta =-0.087; 95% CI: -0.173, -0.001; p = 0.047). Carbamate exposure of maternal and children at both three and seven years old had negative associations with IQP (beta = -0.089; 95% CI: -0.171, -0.007; p = 0.034), and IQFS (beta = -0.064; 95% CI: -0.127, -0.000; p = 0.049) of children at age of seven.Conclusion: Results of the present study verify that children in an agricultural region of China were widely exposed to carbamate pesticides. Carbamate exposure in utero and at three and seven years may adversely impact children's neurodevelopment.
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