| 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. |
- Botvinik-Nezer, Rotem, et al.
(författare)
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Variability in the analysis of a single neuroimaging dataset by many teams
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 582, s. 84-88
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Tidskriftsartikel (refereegranskat)abstract
- Data analysis workflows in many scientific domains have become increasingly complex and flexible. Here we assess the effect of this flexibility on the results of functional magnetic resonance imaging by asking 70 independent teams to analyse the same dataset, testing the same 9 ex-ante hypotheses(1). The flexibility of analytical approaches is exemplified by the fact that no two teams chose identical workflows to analyse the data. This flexibility resulted in sizeable variation in the results of hypothesis tests, even for teams whose statistical maps were highly correlated at intermediate stages of the analysis pipeline. Variation in reported results was related to several aspects of analysis methodology. Notably, a meta-analytical approach that aggregated information across teams yielded a significant consensus in activated regions. Furthermore, prediction markets of researchers in the field revealed an overestimation of the likelihood of significant findings, even by researchers with direct knowledge of the dataset(2-5). Our findings show that analytical flexibility can have substantial effects on scientific conclusions, and identify factors that may be related to variability in the analysis of functional magnetic resonance imaging. The results emphasize the importance of validating and sharing complex analysis workflows, and demonstrate the need for performing and reporting multiple analyses of the same data. Potential approaches that could be used to mitigate issues related to analytical variability are discussed. The results obtained by seventy different teams analysing the same functional magnetic resonance imaging dataset show substantial variation, highlighting the influence of analytical choices and the importance of sharing workflows publicly and performing multiple analyses.
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| 3. |
- Chen, Qinyu, et al.
(författare)
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An Efficient Accelerator for Multiple Convolutions From the Sparsity Perspective
- 2020
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Ingår i: IEEE Transactions on Very Large Scale Integration (vlsi) Systems. - : Institute of Electrical and Electronics Engineers (IEEE). - 1063-8210 .- 1557-9999. ; 28:6, s. 1540-1544
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Tidskriftsartikel (refereegranskat)abstract
- Convolutional neural networks (CNNs) have emerged as one of the most popular ways applied in many fields. These networks deliver better performance when going deeper and larger. However, the complicated computation and huge storage impede hardware implementation. To address the problem, quantized networks are proposed. Besides, various convolutional structures are designed to meet the requirements of different applications. For example, compared with the traditional convolutions (CONVs) for image classification, CONVs for image generation are usually composed of traditional CONVs, dilated CONVs, and transposed CONVs, leading to a difficult hardware mapping problem. In this brief, we translate the difficult mapping problem into the sparsity problem and propose an efficient hardware architecture for sparse binary and ternary CNNs by exploiting the sparsity and low bit-width characteristics. To this end, we propose an ineffectual data removing (IDR) mechanism to remove both the regular and irregular sparsity based on dual-channel processing elements (PEs). Besides, a flexible layered load balance (LLB) mechanism is introduced to alleviate the load imbalance. The accelerator is implemented with 65-nm technology with a core size of 2.56 mm(2). It can achieve 3.72-TOPS/W energy efficiency at 50.1 mW, which makes it a promising design for embedded devices.
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| 4. |
- Zhang, Ruyang, et al.
(författare)
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Independent Validation of Early-Stage Non-Small Cell Lung Cancer Prognostic Scores Incorporating Epigenetic and Transcriptional Biomarkers With Gene-Gene Interactions and Main Effects
- 2020
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Ingår i: Chest. - : Elsevier BV. - 0012-3692. ; 158:2, s. 808-819
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Tidskriftsartikel (refereegranskat)abstract
- Background: DNA methylation and gene expression are promising biomarkers of various cancers, including non-small cell lung cancer (NSCLC). Besides the main effects of biomarkers, the progression of complex diseases is also influenced by gene-gene (G×G) interactions. Research Question: Would screening the functional capacity of biomarkers on the basis of main effects or interactions, using multiomics data, improve the accuracy of cancer prognosis? Study Design and Methods: Biomarker screening and model validation were used to construct and validate a prognostic prediction model. NSCLC prognosis-associated biomarkers were identified on the basis of either their main effects or interactions with two types of omics data. A prognostic score incorporating epigenetic and transcriptional biomarkers, as well as clinical information, was independently validated. Results: Twenty-six pairs of biomarkers with G×G interactions and two biomarkers with main effects were significantly associated with NSCLC survival. Compared with a model using clinical information only, the accuracy of the epigenetic and transcriptional biomarker-based prognostic model, measured by area under the receiver operating characteristic curve (AUC), increased by 35.38% (95% CI, 27.09%-42.17%; P = 5.10 × 10–17) and 34.85% (95% CI, 26.33%-41.87%; P = 2.52 × 10–18) for 3- and 5-year survival, respectively, which exhibited a superior predictive ability for NSCLC survival (AUC3 year, 0.88 [95% CI, 0.83-0.93]; and AUC5 year, 0.89 [95% CI, 0.83-0.93]) in an independent Cancer Genome Atlas population. G×G interactions contributed a 65.2% and 91.3% increase in prediction accuracy for 3- and 5-year survival, respectively. Interpretation: The integration of epigenetic and transcriptional biomarkers with main effects and G×G interactions significantly improves the accuracy of prognostic prediction of early-stage NSCLC survival.
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| 5. |
- Zhang, Tianji, et al.
(författare)
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Glycosaminoglycans in biological samples : towards identification of novel biomarkers
- 2020
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Ingår i: TrAC. Trends in analytical chemistry. - : Elsevier BV. - 0165-9936 .- 1879-3142. ; 122
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Forskningsöversikt (refereegranskat)abstract
- Glycosaminoglycans (GAGs) are unbranched polyanionic polysaccharides involved in a wide spectrum of biological activities. Accumulation and/or structural alteration of GAGs in biological samples have been found correlated with diseases, making these molecules potential biomarkers for the diagnosis of these diseases and monitoring treatment effects. Detection and structural characterization of GAGs in biological samples have been challenging mainly due to their low abundance, structural complexity and heterogeneity. It is highly demanding to develop robust and reliable methodologies for structural characterization and quantification of GAGs, not only for research purposes, but most importantly for pharmaceutical and potential clinical applications, including pharmacokinetic studies for GAGs based drugs and identification of novel biomarkers. In this review, we have collected currently available techniques for detection and analysis of GAGs in biological samples, advantages and drawbacks of these techniques are discussed. Specially, perspectives of the developing methods for GAGs are reviewed.
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| 6. |
- Zhang, Tianji, et al.
(författare)
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Oligosaccharides mapping of nitrous acid degraded heparin through UHPLC-HILIC/WAX-MS
- 2020
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Ingår i: Carbohydrate Polymers. - : Elsevier. - 0144-8617 .- 1879-1344. ; 231
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Tidskriftsartikel (refereegranskat)abstract
- Building blocks characterization is a significant approach for understanding the molecular structure of heparin and its derivatives. Nitrous acid (HONO) depolymerization of heparin generates oligosaccharides that maintain the epimerization conformation on C5 of the uronic acids, reflecting the authentic structure of the parental chain. HONO treatment at pH 1.5 selectively cleaves the bond between N-sulfated glucosamine and hexuronic acid, resulting mainly disaccharides, as well as tetra-, tri-, and mono-saccharides. The tetrasaccharides are derived from the structure of N-acetylated domains while tri-, and mono-saccharides are derived from the reducing or the non-reducing end of the heparin chain. The resulted oligosaccharides were separated and analyzed using a UHPLC-HILIC/WAX-MS method. We succeeded in the identification of 19 tetrasaccharides, 19 trisaccharides and 4 monosaccharides species, majority of which is structurally characterized. By comparing the theoretical possibilities and actual occurrence of the well-characterized tetrasaccharides, we demonstrated that the biosynthesis of heparin is a systematic process.
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| 7. |
- Zhang, Xuning, et al.
(författare)
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On the understanding of energy loss and device fill factor trade-offs in non-fullerene organic solar cells with varied energy levels
- 2020
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Ingår i: Nano Energy. - : ELSEVIER. - 2211-2855 .- 2211-3282. ; 75
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Tidskriftsartikel (refereegranskat)abstract
- Fill factor (FF) is an important parameter governing the power conversion efficiency (PCE) in non-fullerene organic solar cells (NF-OSCs), which however is less studied than the other two parameters (short-circuit current J(sc) and open-circuit voltage V-oc). To understand how energy offsets, exciton and charge carrier dynamics impact the FF, four groups of bulk heterojunctions (BHJs) NF-OSCs are investigated with FFs varying from 0.61 to 0.78 under progressive changes of HOMO-HOMO offsets (Delta(HOMOs), from 0.09 to 0.24 eV). By pump-probe optical spectroscopy, we find that the FF exhibits a positive dependence on Delta(HOMO) and charge-separated state lifetime (tau(CS)) in the blends, a result of inhibited back charge transfers and recombination at the donor-acceptor interface under higher Delta(HOMO)s. Moreover, we observe a fast charge extraction with decreased sensitivity to internal electric-fields in high-FF devices. Despite these merits, the gains of FF are at the expense of increasing the voltage loss to non-radiative recombination in our studied systems. The combined results suggest that remaining appropriate energetic offsets is essential for controlling the carrier dynamics with longer-lived CS-states, restraining charge back transfer and reducing charge recombination toward high FFs and photovoltaic efficiencies.
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| 8. |
- Zhao, Yang, et al.
(författare)
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Enhancement of the summer extreme precipitation over North China by interactions between moisture convergence and topographic settings
- 2020
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Ingår i: Climate Dynamics. - : Springer Science and Business Media LLC. - 0930-7575 .- 1432-0894. ; 54, s. 2713-2730
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Tidskriftsartikel (refereegranskat)abstract
- © 2020, The Author(s). This study investigates the roles of atmospheric moisture transport under the influence of topography for summer extreme precipitation over North China (NC) during 1979–2016. Based on rain gauge precipitation data and a reanalysis, 38 extreme precipitation days in NC during the 38years were selected and associated moisture fluxes estimated. The results show that there is a dominant moisture influx of 311.8kgm−1s−1 into NC along its southern boundary from tropical oceans, and a secondary influx of 107.9kgm−1s−1 across its western boundary carried by mid-latitude westerlies. The outflux across the eastern boundary is 206.9kgm−1s−1 and across the northern boundary is 76.0kgm−1s−1, giving a net moisture gain over NC of 136.8kgm−1s−1. During extreme precipitation days, the moisture flux convergence (MFC) was much larger, exceeding 4 × 10−5kgm−1s−1. The MFC maximum core, the pronounced moisture transport, and the striking extreme precipitation zone over NC are all anchored to the east of the steep slopes of the surrounding topography. Moreover, a remarkably high humidity and strong upward motion also occur near steep slopes, indicating the critical role of the adjacent topography on the extreme precipitations. Simulations with and without the topography in NC using the Weather and Research Forecasting model for six selected out of the 38 extreme precipitation days demonstrate that the surrounding topography reinforces the MFC over NC by 16% relative to the case without terrain, primarily through enhanced wind convergence and higher moisture content, as well as stronger vertical motion induced by diabatic heating. The interactions between moisture convergence and topographic settings strengthen the extreme precipitation over NC.
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| 9. |
- Cai, Yunhao, et al.
(författare)
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Effect of the Energy Offset on the Charge Dynamics in Nonfullerene Organic Solar Cells
- 2020
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Ingår i: ACS Applied Materials and Interfaces. - : AMER CHEMICAL SOC. - 1944-8244 .- 1944-8252. ; 12:39, s. 43984-43991
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Tidskriftsartikel (refereegranskat)abstract
- The energy offset, considered as the driving force for charge transfer between organic molecules, has significant effects on both charge separation and charge recombination in organic solar cells. Herein, we designed material systems with gradually shifting energy offsets, including both positive and negative values. Time-resolved spectroscopy was used to monitor the charge dynamics within the bulk heterojunction. It is striking to find that there is still charge transfer and charge generation when the energy offset reached -0.10 eV (ultraviolet photoelectron spectroscopy data). This work not only indicates the feasibility of the free carrier generation and the following charge separation under the condition of a negative offset but also elucidates the relationship between the charge transfer and the energy offset in the case of polymer chlorination.
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| 10. |
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