| 1. |
- Li, Xian, et al.
(författare)
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GCDB-UNet : A novel robust cloud detection approach for remote sensing images
- 2022
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Ingår i: Knowledge-Based Systems. - : Elsevier BV. - 0950-7051 .- 1872-7409. ; 238
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Tidskriftsartikel (refereegranskat)abstract
- Cloud detection is a prerequisite in many remote sensing applications, and it has been tackled through different approaches from simple thresholding to complicated deep network training. On the other hand, existing approaches are susceptible to failures while handling thin clouds, largely because of their small sizes, sparse distributions, as well as high transparency and similarity to the non-cloud background regions. This paper presents global context dense block U-Net (GCDB-UNet), a robust cloud detection network that embeds global context dense block (GCDB) into the U-Net framework and is capable of detecting thin clouds effectively. GCDB consists of two feature extraction units for addressing the challenges in thin cloud detection, namely, a non-local self-attention unit that extracts sample correlation features by aggregating the sparsely distributed thin clouds and a squeeze excitation unit that extracts channel correlated features by differentiating their importance. In addition, a dense connection scheme is designed to exploit the multi-level fine-grained representations from the two types of extracted features and a recurrent refinement module is introduced for gradual enhancement of the predicted classification map. We also created a fully annotated cloud detection MODIS dataset that consists of 1192 training images, 80 validation images and 150 test images. Extensive experiments on Landsat8, SPARCS and MODIS datasets show that the proposed GCDB-UNet achieves superior cloud detection performance as compared with state-of-the-art methods. Our created MODIS cloud detection dataset is available at https://github.com/xiachangxue/MODIS-Dataset-for-Cloud-Detection.
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| 2. |
- Nie, Man, et al.
(författare)
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The dual role of CD70 in B‐cell lymphomagenesis
- 2022
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Ingår i: Clinical and Translational Medicine. - : John Wiley & Sons. - 2001-1326. ; 12:12
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundCD70 is a costimulatory molecule that is transiently expressed on a small set of activated lymphocytes and is involved in T-cell-mediated immunity. However, the role of CD70 in B-cell malignancies remains controversial.MethodsWe investigated the clinical relevance of CD70 genetic alterations and its protein expression in two diffuse large B-cell lymphoma (DLBCL) cohorts with different ethnic backgrounds. We also performed transcriptomic analysis to explore the role of CD70 alterations in tumour microenvironment. We further tested the blockade of CD70 in combination with PD-L1 inhibitor in a murine lymphoma model.ResultsWe showed that CD70 genetic aberrations occurred more frequently in the Chinese DLBCL cohort (56/233, 24.0%) than in the Swedish cohort (9/84, 10.8%), especially in those with concomitant hepatitis B virus (HBV) infection. The CD70 genetic changes in DLBCL resulted in a reduction/loss of protein expression and/or CD27 binding, which might impair T cell priming and were independently associated with poor overall survival. Paradoxically, we observed that over-expression of CD70 protein was also associated with a poor treatment response, as well as an advanced disease stage and EBV infection. More exhausted CD8+ T cells were furthermore identified in CD70 high-expression DLBCLs. Finally, in a murine lymphoma model, we demonstrated that blocking the CD70/CD27 and/or PD1/PD-L1 interactions could reduce CD70+ lymphoma growth in vivo, by directly impairing the tumour cell proliferation and rescuing the exhausted T cells.ConclusionsOur findings suggest that CD70 can play a role in either tumour suppression or oncogenesis in DLBCL, likely via distinct immune evasion mechanisms, that is, impairing T cell priming or inducing T cell exhaustion. Characterisation of specific dysfunction of CD70 in DLBCL may thus provide opportunities for the development of novel targeted immuno-therapeutic strategies.
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| 3. |
- Pecori, Riccardo, et al.
(författare)
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ADAR1-mediated RNA editing promotes B cell lymphomagenesis
- 2023
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Ingår i: iScience. - : Cell Press. - 2589-0042. ; 26:6
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Tidskriftsartikel (refereegranskat)abstract
- Diffuse large B cell lymphoma (DLBCL) is one of the most common types of aggressive lymphoid malignancies. Here, we explore the contribution of RNA editing to DLBCL pathogenesis. We observed that DNA mutations and RNA editing events are often mutually exclusive, suggesting that tumors can modulate pathway outcomes by altering sequences at either the genomic or the transcriptomic level. RNA editing targets transcripts within known disease-driving pathways such as apoptosis, p53 and NF-kappa B signaling, as well as the RIG-I-like pathway. In this context, we show that ADAR1-mediated editing within MAVS transcript positively correlates with MAVS protein expression levels, associating with increased interferon/NF-kappa B signaling and T cell exhaustion. Finally, using targeted RNA base editing tools to restore editing within MAVS 3 ' UTR in ADAR1-deficient cells, we demonstrate that editing is likely to be causal to an increase in downstream signaling in the absence of activation by canonical nucleic acid receptor sensing.
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| 4. |
- Yang, Jin, et al.
(författare)
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Climatic Forcing of Plio-Pleistocene Formation of the Modern Limpopo River, South Africa
- 2021
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Ingår i: Geophysical Research Letters. - : American Geophysical Union (AGU). - 0094-8276 .- 1944-8007. ; 48:14
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Tidskriftsartikel (refereegranskat)abstract
- Understanding the evolution of river systems in southern Africa is fundamental to constrain the evolution of landscape and sediment dispersal patterns. It is widely considered that the upper Zambezi River was connected with the Limpopo River during the Cretaceous, forming what was then the largest river in Africa. Crustal flexure during the Paleogene severed the upper Zambezi drainage from the Limpopo, setting the framework of the modern Zambezi and Limpopo River systems. We present first evidence-based on heavy-mineral assemblages from cores drilled offshore of the Limpopo River mouth and samples collected in different reaches of the modern Limpopo River, integrated with magnetic susceptibility, detrital-zircon geochronology, and geomorphological analysis-suggesting that the current Limpopo River formed recently in the Plio-Quaternary. Plio-Quaternary climate change is envisaged to have controlled the recent dynamics of river drainage and consequent distribution of sediment loads, as observed in many other transcontinental rivers worldwide.
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| 5. |
- Braun, Emelie, et al.
(författare)
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Comprehensive cell atlas of the first-trimester developing human brain
- 2023
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 382:6667, s. 172-
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Tidskriftsartikel (refereegranskat)abstract
- The adult human brain comprises more than a thousand distinct neuronal and glial cell types, a diversity that emerges during early brain development. To reveal the precise sequence of events during early brain development, we used single-cell RNA sequencing and spatial transcriptomics and uncovered cell states and trajectories in human brains at 5 to 14 postconceptional weeks (pcw). We identified 12 major classes that are organized as ~600 distinct cell states, which map to precise spatial anatomical domains at 5 pcw. We described detailed differentiation trajectories of the human forebrain and midbrain and found a large number of region-specific glioblasts that mature into distinct pre-astrocytes and pre–oligodendrocyte precursor cells. Our findings reveal the establishment of cell types during the first trimester of human brain development.
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| 6. |
- Chong, Hui, et al.
(författare)
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Organo-ptii complexes for potent photodynamic inactivation of multi-drug resistant bacteria and the influence of configuration
- 2024
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Ingår i: Advanced Science. - : John Wiley & Sons. - 2198-3844. ; 11:14
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Tidskriftsartikel (refereegranskat)abstract
- PtII based organometallic photosensitizers (PSs) have emerged as novel potent photodynamic inactivation (PDI) reagents through their enhanced intersystem crossing (ISC) processes. Currently, few PtII PSs have been investigated as antibacterial materials, with relatively poor performances reported and with structure-activity relationships not well described. Herein, a pair of configurational isomers are reported of Bis-BODIPY (4,4-difluoro-boradizaindacene) embedded PtII PSs. The cis-isomer (cis-BBP) displayed enhanced 1O2 generation and better bacterial membrane anchoring capability as compared to the trans-isomer (trans-BBP). The effective PDI concentrations (efficiency > 99.9%) for cis-BBP in Acinetobacter baumannii (multi-drug resistant (MDR)) and Staphylococcus aureus are 400 nM (12 J cm−2) and 100 nM (18 J cm−2), respectively; corresponding concentrations and light doses for trans-BBP in the two bacteria are 2.50 µM (30 J cm−2) and 1.50 µM (18 J cm−2), respectively. The 50% and 90% minimum inhibitory concentration (MIC50 and MIC90) ratio of trans-BBP to cis-BBP is 22.22 and 24.02 in A. baumannii (MDR); 21.29 and 22.36 in methicillin resistant S. aureus (MRSA), respectively. Furthermore, cis-BBP displays superior in vivo antibacterial performance, with acceptable dark and photoinduced cytotoxicity. These results demonstrate cis-BBP is a robust light-assisted antibacterial reagent at sub-micromolecular concentrations. More importantly, configuration of PtII PSs should be an important issue to be considered in further PDI reagents design.
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| 7. |
- Cui, Peng, et al.
(författare)
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Hypothalamic DNA methylation in rats with dihydrotestosterone-induced polycystic ovary syndrome: effects of low-frequency electro-acupuncture.
- 2018
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Ingår i: Experimental physiology. - 1469-445X. ; 103:12, s. 1618-1632
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Tidskriftsartikel (refereegranskat)abstract
- What is the central question of this study? What is the role of hypothalamic DNA methylation in the development of PCOS and the response to electro-acupuncture treatment. What is the main finding and its importance? Global DNA methylation and expression of DNA methyltransferases (Dnmts) were increased in PCOS-like rats, and electro-acupuncture decreased global DNA methylation and Dnmt3b expression. Pyrosequencing showed that the DNA methylation of some PCOS candidate genes was changed in the PCOS and PCOS+EA groups, suggesting that hypothalamic DNA methylation plays an important role in the development of PCOS and in mediating the effects of electro-acupuncture treatment.Polycystic ovary syndrome (PCOS) is a common reproductive and endocrine disease of unknown etiology. Recently, epigenetic studies focusing on DNA methylation in PCOS have received much attention, but the mechanisms are still unclear. In the present study, we used the 5a-dihydrotestosterone-induced PCOS-like rat model and treated the rats with electro-acupuncture (EA). Rats were randomly divided into four groups - controls, diet-induced obesity (DIO), PCOS, and PCOS+EA. We examined the reproductive, metabolic, and behavioral phenotypes, validated the effect of EA, and explored the role of hypothalamic DNA methylation by analyzing the methylation of global DNA and selected candidate genes. The PCOS rats presented with reproductive dysfunctions such as lack of regular estrus cyclicity, metabolic disorders such as increased body weight and insulin resistance, and depression and anxiety-like behaviors. EA improved the reproductive functions, decreased body weight, and improved experimental depressive behavior. Furthermore, global DNA methylation and the expression of DNA methyltransferases (Dnmts) were increased in PCOS rats compared to the control group, and EA decreased the global DNA methylation and the expression of Dnmt3b. In addition, pyrosequencing showed that the DNA methylation of certain CpG sites in targeted genes (Plcg1, Camk2b, Esr2, and Pgr) was increased in the PCOS group, but the DNA methylation of Camk2b and Ar was decreased after EA treatment. These results indicate that hypothalamic DNA methylation might be correlated with the development of PCOS and that EA has an effect on hypothalamic DNA methylation in PCOS rats. This article is protected by copyright. All rights reserved.
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| 8. |
- Lázár, Enikő, et al.
(författare)
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Spatial Dynamics of the Developing Human Heart
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Heart development relies on a topologically defined interplay between a diverse array of cardiac cells. We finely curated spatial and single-cell measurements with subcellular imaging-based transcriptomics validation to explore spatial dynamics during early human cardiogenesis. Analyzing almost 80,000 individual cells and 70,000 spatially barcoded tissue regions between the 5.5th and 14th postconceptional weeks, we identified 31 coarse- and 72 fine-grained cell states and mapped them to highly resolved cardiac cellular niches. We provide novel insight into the development of the cardiac pacemaker-conduction system, heart valves, and atrial septum, and decipher heterogeneity of the hitherto elusive cardiac fibroblast population. Furthermore, we describe the formation of cardiac autonomic innervation and present the first spatial account of chromaffin cells in the fetal human heart. In summary, our study delineates the cellular and molecular landscape of the developing heart’s architecture, offering links to genetic causes of heart disease.
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| 9. |
- Li, Xiaofei, et al.
(författare)
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Important structural factors controlling the conductance of DNA pairs in molecular junctions
- 2010
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Ingår i: The Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 114:33, s. 14240-14242
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Tidskriftsartikel (refereegranskat)abstract
- It has been demonstrated experimentally that DNA base pairs and sequences can be identified by measuring their current changes in metal junctions. We report here a first principles study on electron transport properties of DNA base pairs in gold metal junctions. It is found that the experimentally observed electrode-separation-width-dependent current changes of DNA base pairs are not due to the difference in number of hydrogen bonds involved in different base pairs as proposed in earlier experimental studies but caused by the difference in their stacking structures. It reveals that such an electronic read-out technique is not exact, but practically useful since the statistically favorable misaligned junctions do show distinct dependence on the character of the base pair.
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| 10. |
- Li, Xiaofei, et al.
(författare)
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Profiling spatiotemporal gene expression of the developing human spinal cord and implications for ependymoma origin
- 2023
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Ingår i: Nature Neuroscience. - : Springer Nature. - 1097-6256 .- 1546-1726. ; 26:5, s. 891-901
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Tidskriftsartikel (refereegranskat)abstract
- The authors created a comprehensive developmental cell atlas for spatiotemporal gene expression of the human spinal cord, revealed species-specific regulation during development and used the atlas to infer novel markers for pediatric ependymomas. The spatiotemporal regulation of cell fate specification in the human developing spinal cord remains largely unknown. In this study, by performing integrated analysis of single-cell and spatial multi-omics data, we used 16 prenatal human samples to create a comprehensive developmental cell atlas of the spinal cord during post-conceptional weeks 5-12. This revealed how the cell fate commitment of neural progenitor cells and their spatial positioning are spatiotemporally regulated by specific gene sets. We identified unique events in human spinal cord development relative to rodents, including earlier quiescence of active neural stem cells, differential regulation of cell differentiation and distinct spatiotemporal genetic regulation of cell fate choices. In addition, by integrating our atlas with pediatric ependymomas data, we identified specific molecular signatures and lineage-specific genes of cancer stem cells during progression. Thus, we delineate spatiotemporal genetic regulation of human spinal cord development and leverage these data to gain disease insight.
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