| 1. |
- Campbell, PJ, et al.
(författare)
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Pan-cancer analysis of whole genomes
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82-
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Tidskriftsartikel (refereegranskat)abstract
- Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1–3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4–5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10–18.
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| 2. |
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| 3. |
- Huang, Dan, et al.
(författare)
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Applications of spouted bed technology in the drying of food products
- 2023
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Ingår i: LWT. - 0023-6438. ; 182
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Forskningsöversikt (refereegranskat)abstract
- This study reviews the recent research progress of spouted bed technology in applications of food products. The pure spouted bed drying, spouted bed drying with inert particles and drying carriers and the combination of spouted bed with other drying methods are discussed in detail. Results showed that the effect of temperature on drying characteristics and quality was the most investigated and different results of the drying quality were observed. SBD is a potential drying method for food products, however, there are still some difficulties that limit its industrial application. Thus, modified spouted beds that facilitates scale-up are needed, such as rectangular spouted bed, draft spouted bed and mechanically spouted bed. Spouted bed drying with inert particles is a flexible alternative drying technology compared to the spray drying. The effect of using inert particles in spouted bed is good, however, strong friction and long-term use of inert materials will lead to fracture and fragmentation. Thus, drying carriers are often added. The drying performance and quality of spouted bed with other drying methods is generally better than that of pure spouted bed drying as it combines the advantages of different drying methods.
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| 4. |
- Haghighi, Mona, et al.
(författare)
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A Comparison of Rule-based Analysis with Regression Methods in Understanding the Risk Factors for Study Withdrawal in a Pediatric Study
- 2016
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 6
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Tidskriftsartikel (refereegranskat)abstract
- Regression models are extensively used in many epidemiological studies to understand the linkage between specific outcomes of interest and their risk factors. However, regression models in general examine the average effects of the risk factors and ignore subgroups with different risk profiles. As a result, interventions are often geared towards the average member of the population, without consideration of the special health needs of different subgroups within the population. This paper demonstrates the value of using rule-based analysis methods that can identify subgroups with heterogeneous risk profiles in a population without imposing assumptions on the subgroups or method. The rules define the risk pattern of subsets of individuals by not only considering the interactions between the risk factors but also their ranges. We compared the rule-based analysis results with the results from a logistic regression model in The Environmental Determinants of Diabetes in the Young (TEDDY) study. Both methods detected a similar suite of risk factors, but the rule-based analysis was superior at detecting multiple interactions between the risk factors that characterize the subgroups. A further investigation of the particular characteristics of each subgroup may detect the special health needs of the subgroup and lead to tailored interventions.
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| 5. |
- Huang, Xing, et al.
(författare)
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Semiconducting Conjugated Coordination Polymer with High Charge Mobility Enabled by "4+2" Phenyl Ligands
- 2023
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Ingår i: Journal of the American Chemical Society. - : AMER CHEMICAL SOC. - 0002-7863 .- 1520-5126. ; 145:4, s. 2430-2438
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Tidskriftsartikel (refereegranskat)abstract
- Electrically conductive coordination polymers and metal-organic frameworks are attractive emerging electroactive materials for (opto-)electronics. However, developing semiconducting coordination polymers with high charge carrier mobility for devices remains a major challenge, urgently requiring the rational design of ligands and topological networks with desired electronic structures. Herein, we demonstrate a strategy for synthesizing high-mobility semiconducting conjugated coordination polymers (c-CPs) utilizing novel conjugated ligands with D2h symmetry, namely, "4 + 2" phenyl ligands. Compared with the conventional phenyl ligands with C6h symmetry, the reduced symmetry of the "4 + 2" ligands leads to anisotropic coordination in the formation of c-CPs. Consequently, we successfully achieve a single-crystalline three-dimensional (3D) c-CP Cu4DHTTB (DHTTB = 2,5-dihydroxy-1,3,4,6-tetrathiolbenzene), containing orthogonal ribbon-like pi-d conjugated chains rather than 2D conjugated layers. DFT calculation suggests that the resulting Cu4DHTTB exhibits a small band gap (similar to 0.2 eV), strongly dispersive energy bands near the Fermi level with a low electron-hole reduced effective mass (similar to 0.2m0*). Furthermore, the four-probe method reveals a semiconducting behavior with a decent conductivity of 0.2 S/cm. Thermopower measurement suggests that it is a p-type semiconductor. Ultrafast terahertz photoconductivity measurements confirm Cu4DHTTB's semiconducting nature and demonstrate the Drude-type transport with high charge carrier mobilities up to 88 +/- 15 cm2 V-1 s-1, outperforming the conductive 3D coordination polymers reported till date. This molecular design strategy for constructing high-mobility semiconducting c-CPs lays the foundation for achieving high-performance c-CP-based (opto-)electronics.
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| 6. |
- Kristanl, Matej, et al.
(författare)
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The Seventh Visual Object Tracking VOT2019 Challenge Results
- 2019
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Ingår i: 2019 IEEE/CVF INTERNATIONAL CONFERENCE ON COMPUTER VISION WORKSHOPS (ICCVW). - : IEEE COMPUTER SOC. - 9781728150239 ; , s. 2206-2241
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Konferensbidrag (refereegranskat)abstract
- The Visual Object Tracking challenge VOT2019 is the seventh annual tracker benchmarking activity organized by the VOT initiative. Results of 81 trackers are presented; many are state-of-the-art trackers published at major computer vision conferences or in journals in the recent years. The evaluation included the standard VOT and other popular methodologies for short-term tracking analysis as well as the standard VOT methodology for long-term tracking analysis. The VOT2019 challenge was composed of five challenges focusing on different tracking domains: (i) VOT-ST2019 challenge focused on short-term tracking in RGB, (ii) VOT-RT2019 challenge focused on "real-time" short-term tracking in RGB, (iii) VOT-LT2019 focused on long-term tracking namely coping with target disappearance and reappearance. Two new challenges have been introduced: (iv) VOT-RGBT2019 challenge focused on short-term tracking in RGB and thermal imagery and (v) VOT-RGBD2019 challenge focused on long-term tracking in RGB and depth imagery. The VOT-ST2019, VOT-RT2019 and VOT-LT2019 datasets were refreshed while new datasets were introduced for VOT-RGBT2019 and VOT-RGBD2019. The VOT toolkit has been updated to support both standard short-term, long-term tracking and tracking with multi-channel imagery. Performance of the tested trackers typically by far exceeds standard baselines. The source code for most of the trackers is publicly available from the VOT page. The dataset, the evaluation kit and the results are publicly available at the challenge website(1).
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| 7. |
- Li, Shuai, et al.
(författare)
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Response strategies and biological applications of organic fluorescent thermometry: cell- and mitochondrion-level detection
- 2024
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Ingår i: Analytical Methods. - : ROYAL SOC CHEMISTRY. - 1759-9660 .- 1759-9679.
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Forskningsöversikt (refereegranskat)abstract
- Temperature homeostasis is critical for cells to perform their physiological functions. Among the diverse methods for temperature detection, fluorescent temperature probes stand out as a proven and effective tool, especially for monitoring temperature in cells and suborganelles, with a specific emphasis on mitochondria. The utilization of these probes provides a new opportunity to enhance our understanding of the mechanisms and interconnections underlying various physiological activities related to temperature homeostasis. However, the complexity and variability of cells and suborganelles necessitate fluorescent temperature probes with high resolution and sensitivity. To meet the demanding requirements for intracellular/subcellular temperature detection, several strategies have been developed, offering a range of options to address this challenge. This review examines four fundamental temperature-response strategies employed by small molecule and polymer probes, including intramolecular rotation, polarity sensitivity, Forster resonance energy transfer, and structural changes. The primary emphasis was placed on elucidating molecular design and biological applications specific to each type of probe. Furthermore, this review provides an insightful discussion on factors that may affect fluorescent thermometry, providing valuable perspectives for future development in the field. Finally, the review concludes by presenting cutting-edge response strategies and research insights for mitigating biases in temperature sensing. In this review, we primarily summarized four temperature-response strategies. Then, we further analyzed the chemical modifications and biological applications of the probes. Finally, we have provided a prospective on the future development of probes.
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| 8. |
- Yang, Liting, et al.
(författare)
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Ligand-Directed Conformational Control over Porphyrinic Zirconium Metal-Organic Frameworks for Size-Selective Catalysis
- 2021
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Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 143:31, s. 12129-12137
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Tidskriftsartikel (refereegranskat)abstract
- Zirconium-based metal-organic frameworks (Zr-MOFs) have aroused enormous interest owing to their superior stability, flexible structures, and intriguing functions. Precise control over their crystalline structures, including topological structures, porosity, composition, and conformation, constitutes an important challenge to realize the tailor-made functionalization. In this work, we developed a new Zr-MOF (PCN-625) with a csq topological net, which is similar to that of the well-known PCN-222 and NU-1000. However, the significant difference lies in the conformation of porphyrin rings, which are vertical to the pore surfaces rather than in parallel. The resulting PCN-625 exhibits two types of one-dimensional channels with concrete diameters of 2.03 and 0.43 nm. Furthermore, the vertical porphyrins together with shrunken pore sizes could limit the accessibility of substrates to active centers in the framework. On the basis of the structural characteristics, PCN-625(Fe) can be utilized as an efficient heterogeneous catalyst for the size-selective [4 + 2] hetero-Diels-Alder cycloaddition reaction. Due to its high chemical stability, this catalyst can be repeatedly used over six times. This work demonstrates that Zr-MOFs can serve as tailor-made scaffolds with enhanced flexibility for target-oriented functions.
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| 9. |
- Yuan, Shuai, et al.
(författare)
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Continuous Variation of Lattice Dimensions and Pore Sizes in Metal-Organic Frameworks
- 2020
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Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 142:10, s. 4732-4738
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Tidskriftsartikel (refereegranskat)abstract
- The continuous variation of the lattice metric in metal-organic frameworks (MOFs) allows precise control over their chemical and physical properties. This has been realized herein by a series of mixed-linker and Zr-6-cluster-based MOFs, namely, continuously variable MOFs (CVMOFs). Similar to the substitutional solid solutions, organic linkers with different lengths and various ratios were homogeneously incorporated into a framework rather than being allowed to form separate phases or domains, which was manifested by single-crystal X-ray diffraction, powder X-ray diffraction, fluorescence quenching experiments, and molecular simulations. The unit cell dimension, surface area, and pore size of CVMOFs were precisely controlled by adopting different linker sets and linker ratios. We demonstrate that CVMOFs allow the continuous and fine tailoring of cell-edge lengths from 17.83 to 32.63 angstrom, Brunauer-Emmett-Teller (BET) surface areas from 585 to 3791 m(2)g(-1), and pore sizes up to 15.9 angstrom. Furthermore, this synthetic strategy can be applied to other MOF systems with various metal nodes thus allowing for a variety of CVMOFs with unprecedented tunability.
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| 10. |
- Erickson, Brittany A., et al.
(författare)
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Incorporating Full Elastodynamic Effects and Dipping Fault Geometries in Community Code Verification Exercises for Simulations of Earthquake Sequences and Aseismic Slip (SEAS)
- 2023
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Ingår i: Bulletin of The Seismological Society of America (BSSA). - : SEISMOLOGICAL SOC AMER. - 0037-1106 .- 1943-3573. ; 113:2, s. 499-523
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Tidskriftsartikel (refereegranskat)abstract
- Numerical modeling of earthquake dynamics and derived insight for seismic hazard relies on credible, reproducible model results. The sequences of earthquakes and aseismic slip (SEAS) initiative has set out to facilitate community code comparisons, and verify and advance the next generation of physics-based earthquake models that reproduce all phases of the seis-mic cycle. With the goal of advancing SEAS models to robustly incorporate physical and geo-metrical complexities, here we present code comparison results from two new benchmark problems: BP1-FD considers full elastodynamic effects, and BP3-QD considers dipping fault geometries. Seven and eight modeling groups participated in BP1-FD and BP3-QD, respectively, allowing us to explore these physical ingredients across multiple codes and better understand associated numerical considerations. With new comparison metrics, we find that numerical resolution and computational domain size are critical parameters to obtain matching results. Codes for BP1-FD implement different criteria for switching between quasi-static and dynamic solvers, which require tuning to obtain matching results. In BP3-QD, proper remote boundary conditions consistent with specified rigid body translation are required to obtain matching surface displacements. With these numerical and mathematical issues resolved, we obtain excellent quantitative agreements among codes in earthquake interevent times, event moments, and coseismic slip, with reasonable agreements made in peak slip rates and rupture arrival time. We find that including full inertial effects generates events with larger slip rates and rupture speeds compared to the quasi-dynamic counterpart. For BP3-QD, both dip angle and sense of motion (thrust versus normal faulting) alter ground motion on the hanging and foot walls, and influence event patterns, with some sequences exhibiting similar-size character-istic earthquakes, and others exhibiting different-size events. These findings underscore the importance of considering full elastodynamics and nonvertical dip angles in SEAS models, as both influence short-and long-term earthquake behavior and are relevant to seismic hazard.
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