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| 2. |
- Calabrese, Claudia, et al.
(författare)
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Genomic basis for RNA alterations in cancer
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 578:7793, s. 129-136
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Tidskriftsartikel (refereegranskat)abstract
- Transcript alterations often result from somatic changes in cancer genomes1. Various forms of RNA alterations have been described in cancer, including overexpression2, altered splicing3 and gene fusions4; however, it is difficult to attribute these to underlying genomic changes owing to heterogeneity among patients and tumour types, and the relatively small cohorts of patients for whom samples have been analysed by both transcriptome and whole-genome sequencing. Here we present, to our knowledge, the most comprehensive catalogue of cancer-associated gene alterations to date, obtained by characterizing tumour transcriptomes from 1,188 donors of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA)5. Using matched whole-genome sequencing data, we associated several categories of RNA alterations with germline and somatic DNA alterations, and identified probable genetic mechanisms. Somatic copy-number alterations were the major drivers of variations in total gene and allele-specific expression. We identified 649 associations of somatic single-nucleotide variants with gene expression in cis, of which 68.4% involved associations with flanking non-coding regions of the gene. We found 1,900 splicing alterations associated with somatic mutations, including the formation of exons within introns in proximity to Alu elements. In addition, 82% of gene fusions were associated with structural variants, including 75 of a new class, termed 'bridged' fusions, in which a third genomic location bridges two genes. We observed transcriptomic alteration signatures that differ between cancer types and have associations with variations in DNA mutational signatures. This compendium of RNA alterations in the genomic context provides a rich resource for identifying genes and mechanisms that are functionally implicated in cancer.
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| 3. |
- Deng, Liying, et al.
(författare)
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Can fluorophlogopite mica be used as an alkali metal ion source to boost the growth of two-dimensional molybdenum dioxide?
- 2023
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Ingår i: Applied Surface Science. - : Elsevier BV. - 0169-4332. ; 612
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Tidskriftsartikel (refereegranskat)abstract
- Everyone familiar with two-dimensional (2D) materials is aware of fluorophlogopite mica (FM), which has an atomic-level flat surface that provides an ideal platform for the growth of 2D materials. Since it has been demonstrated that the alkali metal ions (AMI) can aid in the growth of large-sized 2D materials by chemical vapor deposition (CVD) in recent years, it became a major mystery whether FM which contains AMI benefits from them in the preparation of 2D materials by CVD, too. In this article, we dispelled this ambiguity and discovered that temperature is the key for FM as an AMI source to boost the growth of large-sized 2D materials. We carried out variable temperature experiments and found that FM can indeed be incorporated into the growth of large-sized 2D materials as an AMI source at high temperatures and successfully obtained the highly crystalline MoO2 with a larger size compared to those without FM. This finding is of great importance to the understanding of the growth mechanism of FM for 2D materials by CVD and to better exploit its role in the growth of 2D materials.
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| 4. |
- Fang, Xiubo, et al.
(författare)
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Numerical modeling of GaN growth by MOCVD on metal substrate
- 2024
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Ingår i: Digest of Technical Papers - SID International Symposium. - 2168-0159 .- 0097-966X. ; 55:S1, s. 1059-1063
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Konferensbidrag (refereegranskat)abstract
- GaN materials have attracted great interest and have demonstrated remarkable potential in many fields. When growing GaN materials, substrate selection is of great importance. By virtue of their nominally unlimited size, easy removal, and excellent thermal conduction, metal substrates have been suggested as an alternative to the commonly used substrates such as sapphire. GaN growth on metal substrates, however, is still quite rare, and many aspects remain unexplored. This paper uses computational fluid dynamics to perform a three-dimensional numerical simulation of the GaNMOCVD reaction chamber. We investigated the influence of the graphite containers' rotational velocity and the metal matrix's temperature at various locations. When the pressure within the MOCVD chamber remains constant, increasing the graphite tray's rotational velocity enhances the temperature field distribution within the chamber. However, the flow field becomes unstable when the rotation rate exceeds 1000 rpm. Our findings serve as a crucial benchmark for the future parameter optimization of MOCVD growth of GaN on metals.
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| 5. |
- Georgiou, Konstantinos, et al.
(författare)
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Genetic basis of PD-L1 overexpression in diffuse large B-cell lymphomas
- 2016
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Ingår i: Blood. - : American Society of Hematology. - 0006-4971 .- 1528-0020. ; 127:24, s. 3026-3034
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Tidskriftsartikel (refereegranskat)abstract
- Diffuse large B-cell lymphoma (DLBCL) is one of the most common and aggressive types of B-cell lymphoma. Deregulation of proto-oncogene expression after a translocation, most notably to the immunoglobulin heavy-chain locus (IGH), is one of the hallmarks of DLBCL. Using whole-genome sequencing analysis, we have identified the PD-L1/PD-L2 locus as a recurrent translocation partner for IGH in DLBCL. PIM1 and TP63 were also identified as novel translocation partners for PD-L1/PD-L2. Fluorescence in situ hybridization was furthermore used to rapidly screen an expanded DLBCL cohort. Collectively, a subset of samples was found to be affected by gains (12%), amplifications (3%), and translocations (4%) of the PD-L1/PD-L2 locus. RNA sequencing data coupled with immunohistochemistry revealed that these cytogenetic alterations correlated with increased expression of PD-L1 but not of PD-L2. Moreover, cytogenetic alterations affecting the PD-L1/PD-L2 locus were more frequently observed in the non-germinal center B cell-like (non-GCB) subtype of DLBCL. These findings demonstrate the genetic basis of PD-L1 overexpression in DLBCL and suggest that treatments targeting the PD-1-PD-L1/PD-L2 axis might benefit DLBCL patients, especially those belonging to the more aggressive non-GCB subtype.
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| 6. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 7. |
- Pan, Kui, et al.
(författare)
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Highly effective transfer of micro-LED pixels to the intermediate and rigid substrate with weak and tunable adhesion by thiol modification
- 2023
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Ingår i: Nanoscale. - : Royal Society of Chemistry (RSC). - 2040-3372 .- 2040-3364. ; 15:9, s. 4420-4428
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Tidskriftsartikel (refereegranskat)abstract
- Based on transfer printing technology, micro-LED pixels can be transferred to different types and sizes of driving substrates to realize displays with different application scenarios. To achieve a successful transfer, GaN-based micro-LEDs first need to be separated from the original epitaxial substrate. Here, micro-LED pixels (each size 25 μm × 30 μm) on the sapphire substrate were transferred to a flexible semiconductor wafer processing (SWP) tape that is strongly sticky by conventional laser lift-off (LLO) techniques. The pixels on the SWP tape were then transferred by using a sacrificial layer of non-crosslinked oligomeric polystyrene (PS) film onto the intermediate and rigid substrate (IRS) with weak and tunable adhesion by thiol (-SH) modification. The electrode of the micro-LED is Au metal, which forms Au-S bonds with the surface of the IRS to fix the pixels. The rigid substrate helps ensure that the pixel spacing is almost unchanged during the stamp transfer process, and the weak and tunable adhesion facilitates the pixels being picked up by the stamp. The experimental results demonstrate that the pixels can be efficiently transferred to the IRS by LLO and sacrificial layer-assistance, which will provide the possibility of achieving the further transfer of pixels to different types and sizes of driving substrates by a suitable transfer stamp. The transfer process details are discussed, which can provide insights into the transfer of micro-nano devices through polymer sacrificial layers.
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| 8. |
- Pan, Kui, et al.
(författare)
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Monolithically and Vertically Integrated LED-on-FET Device Based on a Novel GaN Epitaxial Structure
- 2023
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Ingår i: IEEE Transactions on Electron Devices. - 1557-9646 .- 0018-9383. ; 70:12, s. 6393-6398
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Tidskriftsartikel (refereegranskat)abstract
- Optoelectronic devices, such as light-emitting diodes (LEDs), based on GaN-based semiconductor compounds are widely used for their advantages of long life, high reliability, and low energy consumption. The persistent challenge is integrating LED with transistors to achieve smaller size, lighter weight, higher speed, and more reliable optoelectronic integrated circuits. Here, we report monolithically and vertically integrated LED-on-FET devices fabricated on a novel GaN epitaxial structure. The designed device structure and fabrication process are simple. It also eliminates the extra area occupied by the transistor, and the shared n-GaN layer between the LED and FET reduces interconnect resistance and improves reliability. The measured threshold voltage (V-Th) of the LED-on-FET device is extrapolated as 3.9 V at the voltage (V-DD) of 5 V, and V-Th decreases with the increase of V-DD . More importantly, the gate voltage (V-GS) shows good performance in modulated electroluminescence (EL) intensity and switching capability of the LED. The integrated LED efficiently emits light modulation with a wavelength of 440 nm at V-DD= 9 V and V-GS=4-9 V (step = 1 V), which are necessary for devices in applications, such as displays and smart lighting. This epitaxy structure and integration scheme is promising in achieving large-scale optoelectronic integrated circuits, such as the next-generation micro-LED and nano-LED with super compact integrated drivers.
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| 9. |
- Pan, Kui, et al.
(författare)
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Ultrasmall-sized light-emitting diodes fabricated by ion implantation based on GaN epitaxial wafers with fully activated or unactivated p-GaN
- 2024
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Ingår i: Optics Letters. - 0146-9592 .- 1539-4794. ; 49:17, s. 4835-4838
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Tidskriftsartikel (refereegranskat)abstract
- A key challenge in realizing ultrahigh-resolution displays is the efficient preparation of ultrasmall-sized (USS) light-emitting diodes (LEDs). Today, GaN-based LEDs are mainly prepared through dry etching processes. However, it is difficult to achieve efficient and controllable etching of USS LED with high aspect ratios, and LED sidewalls will appear after etching, which will have a negative impact on the device itself. Herein, a method for preparing USS LED based on GaN epitaxial wafers is reported (on two types of wafers, i.e., with p-GaN fully activated and unactivated). F−ions are injected into the intentionally exposed areas on the two types of wafers to achieve device isolation. The area under the micro-/nanosized protective masks (0.5, 0.8, 1, 3, 5, 7, 9, and 10 µm wide Ni/Au stripes) are the LED lighting areas. The LED on the p-GaN unactivated wafer (UAW) requires further activation. The Ni/Au mask not only serves as the p-electrode of LED but also Ni as a hydrogen (H) removing metal covering the surface of p-GaN UAW that can desorb H from a Mg element in the film at relatively low temperatures, thereby achieving the selective activation of LED lighting areas. Optoelectronic characterization shows that micro-/nano-sized LED arrays with individual-pixel control were successfully fabricated on the two types of wafers. It is expected that the demonstrated method will provide a new way toward realizing ultrahigh-resolution displays. Analyzing the changes in the current flowing through LED (before and after selective activation) on the F−injected p-GaN UAW, it is believed that depositing H removing metal on p-GaN UAW could possibly realize the device array through the selective activation only (i.e., without the need for ion implantation), offering a completely new insight.
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| 10. |
- 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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