| 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. |
- Lin, Baojun, et al.
(författare)
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Balancing the pre-aggregation and crystallization kinetics enables high efficiency slot-die coated organic solar cells with reduced non-radiative recombination losses
- 2020
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Ingår i: Energy & Environmental Science. - : Royal Society of Chemistry (RSC). - 1754-5692 .- 1754-5706. ; 13:8, s. 2467-2479
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Tidskriftsartikel (refereegranskat)abstract
- Slot-die coating being compatible with the roll-to-roll technique has been regarded as a promising tool for upscaling the manufacturing of organic solar cells (OSCs). However, there has been a significant gap between the efficiencies of the state-of-the-art spin-coated devices and the scalable processed devices. The active layer morphology is crucial to achieve high efficiency in OSCs, which depends on the conditions of film fabrication. To figure out and optimize the slot-die coating process, a deeper understanding of the film formation kinetics is important. Herein, in situ measurements of the slot-die coating process based on the PM7:IT4F system are demonstrated to illustrate the aggregation and crystallization evolution at various die temperatures and substrate temperatures. OSCs with a high power conversion efficiency of 13.2% are achieved at 60 degrees C die temperature/60 degrees C substrate temperature due to the improved exciton dissociation, charge transport and suppressed non-radiative charge recombination. The optimized morphology is attributed to the balanced polymer pre-aggregation and small molecule crystallization kinetics. The unsuitable die temperature leads to overlarge phase separation and consequently inefficient exciton dissociation while the improper substrate temperature results in weak crystallization and the following shrunken carrier lifetime with strong non-radiative combination. This work provides fundamental understanding on the correlations among processing methodology, solution pre-aggregation, morphology formation kinetics, device physics and device performance and affords guidance for device optimization in scalable manufacturing.
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| 3. |
- Liu, Hui, et al.
(författare)
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Centromere-Specific Retrotransposons and Very-Long-Chain Fatty Acid Biosynthesis in the Genome of Yellowhorn (Xanthoceras sorbifolium, Sapindaceae), an Oil-Producing Tree With Significant Drought Resistance
- 2021
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Ingår i: Frontiers in Plant Science. - : Frontiers Media S.A.. - 1664-462X. ; 12
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Tidskriftsartikel (refereegranskat)abstract
- In-depth genome characterization is still lacking for most of biofuel crops, especially for centromeres, which play a fundamental role during nuclear division and in the maintenance of genome stability. This study applied long-read sequencing technologies to assemble a highly contiguous genome for yellowhorn (Xanthoceras sorbifolium), an oil-producing tree, and conducted extensive comparative analyses to understand centromere structure and evolution, and fatty acid biosynthesis. We produced a reference-level genome of yellowhorn, ∼470 Mb in length with ∼95% of contigs anchored onto 15 chromosomes. Genome annotation identified 22,049 protein-coding genes and 65.7% of the genome sequence as repetitive elements. Long terminal repeat retrotransposons (LTR-RTs) account for ∼30% of the yellowhorn genome, which is maintained by a moderate birth rate and a low removal rate. We identified the centromeric regions on each chromosome and found enrichment of centromere-specific retrotransposons of LINE1 and Gypsy in these regions, which have evolved recently (∼0.7 MYA). We compared the genomes of three cultivars and found frequent inversions. We analyzed the transcriptomes from different tissues and identified the candidate genes involved in very-long-chain fatty acid biosynthesis and their expression profiles. Collinear block analysis showed that yellowhorn shared the gamma (γ) hexaploidy event with Vitis vinifera but did not undergo any further whole-genome duplication. This study provides excellent genomic resources for understanding centromere structure and evolution and for functional studies in this important oil-producing plant.
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| 4. |
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| 5. |
- Shen, Ping, et al.
(författare)
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Hypervirulence Markers Among Non-ST11 Strains of Carbapenem- and Multidrug-ResistantKlebsiella pneumoniaeIsolated From Patients With Bloodstream Infections
- 2020
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Ingår i: Frontiers in Microbiology. - : FRONTIERS MEDIA SA. - 1664-302X. ; 11
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Tidskriftsartikel (refereegranskat)abstract
- Multidrug-resistantKlebsiella pneumoniaeand hypervirulentK. pneumoniae(hvKP) have traditionally been considered two individual populations; however, strains displaying both phenotypes have emerged during the recent decade. Understanding the genotypic and phenotypic basis of the convergence could be of clinical importance. In this study, we aimed to evaluate the pathogenicity associated with different combinations of genotypes (i.e., sequence types, virulence factors, and capsular serotypes) and phenotypes (i.e., hypermucoviscosity and drug susceptibility) inK. pneumoniae.A total of 11K. pneumoniaeisolates causing bloodstream infections were included in the study, and they were assigned to seven STs (ST23, ST15, ST268, ST660, ST86, ST65, and ST1660) and carried various K-loci (KL1, KL2, KL16, KL20, and KL24). Hypermucoviscosity was observed for six isolates.bla(KPC-2)was detected in six carbapenem-resistant isolates, and the remaining ones were either multidrug-resistant or resistant to two types of antibiotics. Aerobactin- and yersiniabactin-encoding genes were detected in all isolates. AlthoughrmpA2was detected in all isolates, most contained frameshift mutations (82%). Genes encoding salmochelin, RmpA, and PEG344 were detected in seven isolates. Colibactin-encoding genes were carried by six isolates. Discrepancies among measured virulence inGalleria mellonellaand the serum-killing assay, and genotypes and phenotypes were detected. The results illustrate the complexity and difficulty with the current knowledge of hypervirulence to predict the phenotype by using genetic and phenotypic markers. Additionally, the emergence of carbapenem resistance in two isolates of KPC-2-producing hvKP of different sequence types emphasizes the urgency with which reliable clinical diagnostics for hvKP is needed.
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| 6. |
- Xu, Jie, et al.
(författare)
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UV-B-induced molecular mechanisms of stress physiology responses in the major northern Chinese conifer Pinus tabuliformis Carr
- 2021
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Ingår i: Tree Physiology. - : Oxford University Press. - 0829-318X .- 1758-4469. ; 41:7, s. 1247-1263
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Tidskriftsartikel (refereegranskat)abstract
- During their lifetimes, plants are exposed to different abiotic stress factors eliciting various physiological responses and triggering important defense processes. For UV-B radiation responses in forest trees, the genetics and molecular regulation remain to be elucidated. Here, we exposed Pinus tabuliformis Carr., a major conifer from northern China, to short-term high-intensity UV-B and employed a systems biology approach to characterize the early physiological processes and the hierarchical gene regulation, which revealed a temporal transition from primary to secondary metabolism, the buildup of enhanced antioxidant capacity and stress-signaling activation. Our findings showed that photosynthesis and biosynthesis of photosynthetic pigments were inhibited, while flavonoids and their related derivates biosynthesis, as well as glutathione and glutathione S-transferase mediated antioxidant processes, were enhanced. Likewise, stress-related phytohormones (jasmonic acid, salicylic acid and ethylene), kinase and reactive oxygen species signal transduction pathways were activated. Biological processes regulated by auxin and karrikin were, for the first time, found to be involved in plant defense against UV-B by promoting the biosynthesis of flavonoids and the improvement of antioxidant capacity in our research system. Our work evaluated the physiological and transcriptome perturbations in a conifer's response to UV-B, and generally, highlighted the necessity of a systems biology approach in addressing plant stress biology.
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| 7. |
- Zhou, Guang-Quan, et al.
(författare)
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A Single-Shot Region-Adaptive Network for Myotendinous Junction Segmentation in Muscular Ultrasound Images
- 2020
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Ingår i: IEEE Transactions on Ultrasonics, Ferroelectrics and Frequency Control. - : Institute of Electrical and Electronics Engineers (IEEE). - 0885-3010 .- 1525-8955. ; 67:12, s. 2531-2542
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Tidskriftsartikel (refereegranskat)abstract
- Tracking the myotendinous junction (MTJ) in consecutive ultrasound images is crucial for understanding the mechanics and pathological conditions of the muscletendon unit. However, the lack of reliable and efficient identification of MTJ due to poor image quality and boundary ambiguity restricts its application in motion analysis. In recent years, with the rapid development of deep learning, the region-based convolution neural network (RCNN) has shown great potential in the field of simultaneous objection detection and instance segmentation in medical images. This article proposes a region-adaptive network (RAN) to localize MTJ region and to segment it in a single shot. Our model learns about the salient information of MTJ with the help of a composite architecture. Herein, a region-based multitask learning network explores the region containing MTJ, while a parallel end-to-end U-shaped path extracts the MTJ structure from the adaptively selected region for combating data imbalance and boundary ambiguity. By demonstrating the ultrasound images of the gastrocnemius, we showed that the RAN achieves superior segmentation performance when compared with the state-of-the-art Mask RCNN method with an average Dice score of 80.1. Our proposed method is robust and reliable for advanced muscle and tendon function examinations obtained by ultrasound imaging.
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| 8. |
- Zhou, Guang-Quan, et al.
(författare)
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Automatic Myotendinous Junction Identification in Ultrasound Images Based on Junction-Based Template Measurements
- 2023
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Ingår i: IEEE transactions on neural systems and rehabilitation engineering. - : Institute of Electrical and Electronics Engineers (IEEE). - 1534-4320 .- 1558-0210. ; 31, s. 851-862
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Tidskriftsartikel (refereegranskat)abstract
- Tracking the myotendinous junction (MTJ) motion in consecutive ultrasound images is essential to assess muscle and tendon interaction and understand the mechanics' muscle-tendon unit and its pathological conditions during motion. However, the inherent speckle noises and ambiguous boundaries deter the reliable identification of MTJ, thus restricting their usage in human motion analysis. This study advances a fully automatic displacement measurement method for MTJ using prior shape knowledge on the Y-shape MTJ, precluding the influence of irregular and complicated hyperechoic structures in muscular ultrasound images. Our proposed method first adopts the junction candidate points using a combined measure of Hessian matrix and phase congruency, followed by a hierarchical clustering technique to refine the candidates approximating the position of the MTJ. Then, based on the prior knowledge of Y-shape MTJ, we finally identify the best matching junction points according to intensity distributions and directions of their branches using multiscale Gaussian templates and a Kalman filter. We evaluated our proposed method using the ultrasound scans of the gastrocnemius from 8 young, healthy volunteers. Our results present more consistent with the manual method in the MTJ tracking method than existing optical flow tracking methods, suggesting its potential in facilitating muscle and tendon function examinations with in vivo ultrasound imaging.
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| 9. |
- Zhou, Kai-Xia, et al.
(författare)
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Increased Nuclear Transporter KPNA2 Contributes to Tumor Immune Evasion by Enhancing PD-L1 Expression in PDAC
- 2021
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Ingår i: Journal of Immunology Research. - : Hindawi Limited. - 2314-7156 .- 2314-8861. ; 2021, s. 6694392-6694392
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Tidskriftsartikel (refereegranskat)abstract
- Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest malignancies and is known for its high resistance and low response to treatment. Tumor immune evasion is a major stumbling block in designing effective anticancer therapeutic strategies. Karyopherin alpha 2 (KPNA2), a member of the nuclear transporter family, is elevated in multiple human cancers and accelerates carcinogenesis. However, the specific role of KPNA2 in PDAC remains unclear. In this study, we found that expression of KPNA2 was significantly upregulated in PDAC compared to adjacent nontumor tissue and its high expression was correlated with poor survival outcome by analyzing the GEO datasets. Similar KPNA2 expression pattern was also found in both human patient samples and KPC mouse models through IHC staining. Although KPNA2 knockdown failed to impair the vitality and migration ability of PDAC cells in vitro, the in vivo tumor growth was significantly impeded and the expression of immune checkpoint ligand PD-L1 was reduced by silencing KPNA2. Furthermore, we uncovered that KPNA2 modulated the expression of PD-L1 by mediating nuclear translocation of STAT3. Collectively, our data suggested that KPNA2 has the potential to serve as a promising biomarker for diagnosis in PDAC.
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| 10. |
- Zhou, Yongqiang, et al.
(författare)
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Key factors driving dissolved organic matter composition and bioavailability in lakes situated along the Eastern Route of the South-to-North Water Diversion Project, China
- 2023
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Ingår i: Water Research. - : Elsevier. - 0043-1354 .- 1879-2448. ; 233
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Tidskriftsartikel (refereegranskat)abstract
- The Eastern Route of the South-to-North Water Diversion Project (SNWDP-ER) is a large scale multi-decade infrastructure project aiming to divert substantial amounts of water (approximate to 45 billion m3 yr-1) to alleviate water shortage in comparatively arid regions of northern China. The project has ramifications for hydrological con-nectivity and biogeochemical cycling of dissolved organic matter (DOM) in regional lakes affected by the project. We carried out an extensive field sampling campaign along the SNWDP-ER in different hydrological seasons of 2018 and monthly observations in Lake Hongze and Lake Luoma from April 2018 to June 2021. We found the lakes connecting to the SNWDP-ER had higher mean DOC, specific UV absorbance, higher ratio of humic-like to protein-like fluorophores (Humic : Protein), and shallower spectral slope (S275-295) in the wet season compared to the wet-to-dry transition, and dry seasons. The southern lakes and Yangtze River had lower DOC concen-tration, bioavailable DOC (BDOC), and higher DOM aromaticity compared to the northern two downstream lakes. Ultrahigh-resolution mass spectrometry (FT-ICR MS) revealed higher relative abundance of CHO-containing and aromatic compounds in the Yangtze River and the southern three upstream lakes compared to the northern two lakes. The data from Lake Hongze and Lake Luoma, studied in different hydrological seasons, suggest that water delivery had high consistency in DOM composition and BDOC over the season. We conclude that positioning along the watercourse and seasonally variable hydrological conditions play an important role in influencing the DOM composition and bioavailability of key lakes connecting to the SNWDP-ER. Our results indicated that the water diversion project delivers water with low DOC concentration and higher aromaticity and thus is of higher quality since it has higher DOM removal potential during drinking water treatment.
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