| 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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| 5. |
- 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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| 6. |
- Das, Arkaprava, et al.
(författare)
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Orbital hybridization-induced band offset phenomena in NixCd1-xO thin films
- 2020
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Ingår i: Nanoscale. - : ROYAL SOC CHEMISTRY. - 2040-3364 .- 2040-3372. ; 12:2, s. 669-686
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Tidskriftsartikel (refereegranskat)abstract
- Herein, we present the cationic impurity-assisted band offset phenomena in NixCd1-xO (x = 0, 0.02, 0.05, 0.1, 0.2, 0.4, 0.8, and 1) thin films and further discuss them based on orbital hybridization modification. The compositional and structural studies revealed that the cationic substitution of Cd2+ by Ni2+ ions leads to a monotonic shift in the (220) diffraction peak, indicating the suppression of lattice distortion, while the evolution of local strain with an increase in Ni concentration is mainly associated with the mismatch in the electronegativity of the Cd2+ and Ni2+ ions. In fact, Fermi level pinning towards the conduction band minimum takes place with an increase in the Ni concentration at the cost of electronically compensated oxygen vacancies, resulting in the modification of the distribution of carrier concentration, which eventually affects the band edge effective mass of the conduction band electrons and further endorses band gap renormalization. Besides, the appearance of a longitudinal optical (LO) mode at 477 cm(-1), as manifested by Raman spectroscopy, also indicates the active involvement of electron-phonon scattering, whereas modification in the local coordination environment, particularly anti-crossing interaction in conjunction with the presence of satellite features and shake-up states with Ni doping, was confirmed by X-ray absorption near-edge and X-ray photoelectron spectroscopy studies. These results manifest the gradual reduction of orbital hybridization upon the incorporation of Ni, leading to a decrement in the band edge effective electron mass. Finally, the molecular dynamics simulation reflected a 13% reduction in the lattice parameter for the NiO thin film compared to the undoped film, while the projected density of states calculation further supports the experimental observation of reduced orbital hybridization with an increase in Ni concentration.
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| 7. |
- Das, Arkaprava, et al.
(författare)
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Temperature-Dependent Cationic Doping-Driven Phonon Dynamics Investigation in CdO Thin Films Using Raman Spectroscopy
- 2020
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Ingår i: The Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 124:39, s. 21818-21828
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Tidskriftsartikel (refereegranskat)abstract
- In the present work, undoped cadmium oxide (CdO)- and 1% Tin (Sn)-doped CdO thin films were prepared by the sol-gel route. These samples have been analyzed by temperature (T)-dependent (80-500 K) Raman spectroscopy and studied for their lattice dynamics and vibrational density of states. Results indicate that the room T synthesized pure CdO thin film manifests two prime second order features, that is, 300.5 cm(-1) transverse optical (TO) and 488 cm(-1) longitudinal optical (LO) phonon modes. However, incorporation of cationic-assisted impurity (Sn) with larger ionic radii results in a softening of the high-frequency LO (480.5 cm(-1)) mode via lattice deformation scattering potential. In fact, selective Sn doping increases the carrier concentration in the host CdO matrix which subsequently mitigates intraionic anharmonicity owing to increased Coulomb screening, leading to disappearance of the low-frequency TO mode (300.5 cm(-1)). In the case of pure CdO thin films, surface electron-induced electron-LO phonon coupling causes the intensity enhancement in LO modes, while negligible four-phonon anharmonic coupling results in lowering of full width at half maxima below Debye T. On the other hand, Fruhlich interaction in the polar LO phonon mode supersedes the impact of anharmonic decay and dominates the overall phonon decay process by impurity incorporation, via appropriate Sn doping. Theoretical phonon dispersion profiles throughout the Brillouin zone with increasing T suggests stronger TO phonon mode softening along with optical branch broadening followed by LO-TO splitting. The acoustic branch barely suffers any shift with changing T which cannot be observed in experimental spectra. However, the flexural phonon modes confer a direct indication of changed rigidity and bond stiffness with varying T. Overall, the present investigation provides experimental evidence regarding the significance of Debye T, below and above which the three- and four-phonon anharmonicity are feasible in phonon scattering in conjunction with theoretical insights.
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| 8. |
- Lamba, Tarundeep Kaur, et al.
(författare)
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LSPR anisotropy minimization by sequential growth of Ag nanoparticles on nanoripple patterned Si surface for SERS Application
- 2024
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Ingår i: Surfaces and Interfaces. - 2468-0230. ; 52
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Tidskriftsartikel (refereegranskat)abstract
- The present work describes the formation of low-aspect-ratio Ag nanoparticles (NPs) arrays by sequential deposition of Ag from different growth directions on a nanoripple-patterned Si substrate, produced by low-energy ion beam irradiation. It is observed that the growth of Ag-NPs on ripple surfaces is direction-dependent due to the asymmetric ridge of the ripple pattern. This asymmetric ridge can be utilized to tune the shape of NP from elongated to spherical and in turn, assists in minimizing the LSPR anisotropy. The Finite-Difference-Time-Domain (FDTD) simulations demonstrate that the interparticle gap, major, and minor axis combinations of a NP are crucial in minimizing anisotropic near-field interaction. NPs grown perpendicular to the ripple from either direction lead to an elongated chain of nanoparticles; however, if a proper combination of sequential growth times is chosen then the aspect ratio of NPs can be tuned from elongation to spherical ones. Interestingly, a LSPR shift of 209 nm was observed when NPs are grown for 60 min on ripple patterns from one direction only. On the other hand, it reduces to 54 nm when NPs are sequentially grown for 30 min from each of directions, perpendicular to the ripples. SERS measurements also evidence a minimized anisotropic nature in sequentially grown NP arrays; hence, the growth direction as well as optimized growth times together can be used to control the LSPR anisotropy of NP arrays which can be used to fabricate such isotropic SERS substrates.
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| 9. |
- Leonard, Hampton L., et al.
(författare)
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The IPDGC/GP2 Hackathon - an open science event for training in data science, genomics, and collaboration using Parkinson’s disease data
- 2023
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Ingår i: npj Parkinson's Disease. - : Springer Science and Business Media LLC. - 2373-8057. ; 9:1
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Tidskriftsartikel (refereegranskat)abstract
- Open science and collaboration are necessary to facilitate the advancement of Parkinson’s disease (PD) research. Hackathons are collaborative events that bring together people with different skill sets and backgrounds to generate resources and creative solutions to problems. These events can be used as training and networking opportunities, thus we coordinated a virtual 3-day hackathon event, during which 49 early-career scientists from 12 countries built tools and pipelines with a focus on PD. Resources were created with the goal of helping scientists accelerate their own research by having access to the necessary code and tools. Each team was allocated one of nine different projects, each with a different goal. These included developing post-genome-wide association studies (GWAS) analysis pipelines, downstream analysis of genetic variation pipelines, and various visualization tools. Hackathons are a valuable approach to inspire creative thinking, supplement training in data science, and foster collaborative scientific relationships, which are foundational practices for early-career researchers. The resources generated can be used to accelerate research on the genetics of PD.
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