| 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. |
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| 3. |
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| 4. |
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| 5. |
- Berndt, Sonja, I, et al.
(författare)
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Distinct germline genetic susceptibility profiles identified for common non-Hodgkin lymphoma subtypes
- 2022
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Ingår i: Leukemia. - : Springer Nature. - 0887-6924 .- 1476-5551. ; 36:12, s. 2835-2844
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Tidskriftsartikel (refereegranskat)abstract
- Lymphoma risk is elevated for relatives with common non-Hodgkin lymphoma (NHL) subtypes, suggesting shared genetic susceptibility across subtypes. To evaluate the extent of mutual heritability among NHL subtypes and discover novel loci shared among subtypes, we analyzed data from eight genome-wide association studies within the InterLymph Consortium, including 10,629 cases and 9505 controls. We utilized Association analysis based on SubSETs (ASSET) to discover loci for subsets of NHL subtypes and evaluated shared heritability across the genome using Genome-wide Complex Trait Analysis (GCTA) and polygenic risk scores. We discovered 17 genome-wide significant loci (P < 5 × 10−8) for subsets of NHL subtypes, including a novel locus at 10q23.33 (HHEX) (P = 3.27 × 10−9). Most subset associations were driven primarily by only one subtype. Genome-wide genetic correlations between pairs of subtypes varied broadly from 0.20 to 0.86, suggesting substantial heterogeneity in the extent of shared heritability among subtypes. Polygenic risk score analyses of established loci for different lymphoid malignancies identified strong associations with some NHL subtypes (P < 5 × 10−8), but weak or null associations with others. Although our analyses suggest partially shared heritability and biological pathways, they reveal substantial heterogeneity among NHL subtypes with each having its own distinct germline genetic architecture.
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| 6. |
- Davies, Helen R., et al.
(författare)
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HRDetect is a predictor of BRCA1 and BRCA2 deficiency based on mutational signatures
- 2017
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Ingår i: Nature Medicine. - : Springer Science and Business Media LLC. - 1546-170X .- 1078-8956. ; 23:4, s. 517-525
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Tidskriftsartikel (refereegranskat)abstract
- Approximately 1-5% of breast cancers are attributed to inherited mutations in BRCA1 or BRCA2 and are selectively sensitive to poly(ADP-ribose) polymerase (PARP) inhibitors. In other cancer types, germline and/or somatic mutations in BRCA1 and/or BRCA2 (BRCA1/BRCA2) also confer selective sensitivity to PARP inhibitors. Thus, assays to detect BRCA1/BRCA2-deficient tumors have been sought. Recently, somatic substitution, insertion/deletion and rearrangement patterns, or 'mutational signatures', were associated with BRCA1/BRCA2 dysfunction. Herein we used a lasso logistic regression model to identify six distinguishing mutational signatures predictive of BRCA1/BRCA2 deficiency. A weighted model called HRDetect was developed to accurately detect BRCA1/BRCA2-deficient samples. HRDetect identifies BRCA1/BRCA2-deficient tumors with 98.7% sensitivity (area under the curve (AUC) = 0.98). Application of this model in a cohort of 560 individuals with breast cancer, of whom 22 were known to carry a germline BRCA1 or BRCA2 mutation, allowed us to identify an additional 22 tumors with somatic loss of BRCA1 or BRCA2 and 47 tumors with functional BRCA1/BRCA2 deficiency where no mutation was detected. We validated HRDetect on independent cohorts of breast, ovarian and pancreatic cancers and demonstrated its efficacy in alternative sequencing strategies. Integrating all of the classes of mutational signatures thus reveals a larger proportion of individuals with breast cancer harboring BRCA1/BRCA2 deficiency (up to 22%) than hitherto appreciated (∼1-5%) who could have selective therapeutic sensitivity to PARP inhibition.
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| 7. |
- George, Julie, et al.
(författare)
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Comprehensive genomic profiles of small cell lung cancer
- 2015
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 524:7563, s. 47-U73
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Tidskriftsartikel (refereegranskat)abstract
- We have sequenced the genomes of 110 small cell lung cancers (SCLC), one of the deadliest human cancers. In nearly all the tumours analysed we found bi-allelic inactivation of TP53 and RB1, sometimes by complex genomic rearrangements. Two tumours with wild-type RB1 had evidence of chromothripsis leading to overexpression of cyclin D1 (encoded by the CCND1 gene), revealing an alternative mechanism of Rb1 deregulation. Thus, loss of the tumour suppressors TP53 and RB1 is obligatory in SCLC. We discovered somatic genomic rearrangements of TP73 that create an oncogenic version of this gene, TP73Dex2/3. In rare cases, SCLC tumours exhibited kinase gene mutations, providing a possible therapeutic opportunity for individual patients. Finally, we observed inactivating mutations in NOTCH family genes in 25% of human SCLC. Accordingly, activation of Notch signalling in a pre-clinical SCLC mouse model strikingly reduced the number of tumours and extended the survival of the mutant mice. Furthermore, neuroendocrine gene expression was abrogated by Notch activity in SCLC cells. This first comprehensive study of somatic genome alterations in SCLC uncovers several key biological processes and identifies candidate therapeutic targets in this highly lethal form of cancer.
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| 8. |
- Glodzik, Dominik, et al.
(författare)
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A somatic-mutational process recurrently duplicates germline susceptibility loci and tissue-specific super-enhancers in breast cancers
- 2017
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 49:3, s. 341-348
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Tidskriftsartikel (refereegranskat)abstract
- Somatic rearrangements contribute to the mutagenized landscape of cancer genomes. Here, we systematically interrogated rearrangements in 560 breast cancers by using a piecewise constant fitting approach. We identified 33 hotspots of large (>100 kb) tandem duplications, a mutational signature associated with homologous-recombination-repair deficiency. Notably, these tandem-duplication hotspots were enriched in breast cancer germline susceptibility loci (odds ratio (OR) = 4.28) and breast-specific 'super-enhancer' regulatory elements (OR = 3.54). These hotspots may be sites of selective susceptibility to double-strand-break damage due to high transcriptional activity or, through incrementally increasing copy number, may be sites of secondary selective pressure. The transcriptomic consequences ranged from strong individual oncogene effects to weak but quantifiable multigene expression effects. We thus present a somatic-rearrangement mutational process affecting coding sequences and noncoding regulatory elements and contributing a continuum of driver consequences, from modest to strong effects, thereby supporting a polygenic model of cancer development.
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| 9. |
- Gu, Qiang, et al.
(författare)
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VKORC1-1639G>A, CYP2C9, EPHX1691A>G genotype, body weight, and age are important predictors for warfarin maintenance doses in patients with mechanical heart valve prostheses in southwest China
- 2010
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Ingår i: European Journal of Clinical Pharmacology. - : Springer Science and Business Media LLC. - 0031-6970 .- 1432-1041. ; 66:12, s. 1217-1227
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Tidskriftsartikel (refereegranskat)abstract
- There were great interindividual differences in warfarin maintenance dosage (ranging from 0.6 to 8.4 mg/day) among the 127 patients with mechanical heart valve prostheses. VKORC1-1639G>A, CYP2C9, EPHX1691A>G polymorphism, body weight, and age were found to affect the dose demands. Multiple linear regression models incorporating genetic polymorphisms of VKORC1, CYP2C9, EPHX1691A>G, and the nongenetic factors of age and body weight were developed, and explained up to 76.8% of the total variation (adjusted R (2) of 0.743) in warfarin maintenance doses in southwest Chinese patients with mechanical heart valve prostheses.
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| 10. |
- Khan, F. U., et al.
(författare)
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Antioxidant responses of the mussel Mytilus coruscus co-exposed to ocean acidification, hypoxia and warming
- 2021
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Ingår i: Marine Pollution Bulletin. - : Elsevier BV. - 0025-326X. ; 162:January
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Tidskriftsartikel (refereegranskat)abstract
- In the present study, the combined effects of pH, dissolved oxygen (DO) and temperature levels on the antioxidant responses of the mussel Mytilus coruscus were evaluated. Mussels were exposed to two pH (8.1, 7.7-acidification), two DO (6 mg L−1, 2 mg L−1-hypoxia) and two temperature levels (20 °C, 30 °C-warming) for 30 days. SOD, CAT, MDA, GPx, GSH, GST, TAOC, AKP, ACP, GPT, AST levels were measured in the gills of mussels. All tested biochemical parameters were altered by these three environmental stressors. Values for all the test parameters except GSH first increased and then decreased at various experimental treatments during days 15 and 30 as a result of acidification, hypoxia and warming. GSH content always increased with decreased pH, decreased DO and increased temperature. PCA showed a positive correlation among all the measured biochemical indexes. IBR results showed that M. coruscus were adversely affected by reduced pH, low DO and elevated temperature. © 2020 Elsevier Ltd
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| 11. |
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| 12. |
- Kong, Z., et al.
(författare)
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Growth and Strain Modulation of GeSn Alloys for Photonic and Electronic Applications
- 2022
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Ingår i: Nanomaterials. - : MDPI AG. - 2079-4991. ; 12:6
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Tidskriftsartikel (refereegranskat)abstract
- GeSn materials have attracted considerable attention for their tunable band structures and high carrier mobilities, which serve well for future photonic and electronic applications. This research presents a novel method to incorporate Sn content as high as 18% into GeSn layers grown at 285–320◦C by using SnCl4 and GeH4 precursors. A series of characterizations were performed to study the material quality, strain, surface roughness, and optical properties of GeSn layers. The Sn content could be calculated using lattice mismatch parameters provided by X-ray analysis. The strain in GeSn layers was modulated from fully strained to partially strained by etching Ge buffer into Ge/GeSn heterostructures . In this study, two categories of samples were prepared when the Ge buffer was either laterally etched onto Si wafers, or vertically etched Ge/GeSnOI wafers which bonded to the oxide. In the latter case, the Ge buffer was initially etched step-by-step for the strain relaxation study. Meanwhile, the Ge/GeSn heterostructure in the first group of samples was patterned into the form of micro-disks. The Ge buffer was selectively etched by using a CF4/O2 gas mixture using a plasma etch tool. Fully or partially relaxed GeSn micro-disks showed photoluminescence (PL) at room temperature. PL results showed that red-shift was clearly observed from the GeSn microdisk structure, indicating that the compressive strain in the as-grown GeSn material was partially released. Our results pave the path for the growth of high quality GeSn layers with high Sn content, in addition to methods for modulating the strain for lasing and detection of short-wavelength infrared at room temperature.
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| 13. |
- Li, Cai, et al.
(författare)
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Two Antarctic penguin genomes reveal insights into their evolutionary history and molecular changes related to the Antarctic environment
- 2014
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Ingår i: GigaScience. - 2047-217X. ; 3
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Tidskriftsartikel (refereegranskat)abstract
- Background: Penguins are flightless aquatic birds widely distributed in the Southern Hemisphere. The distinctive morphological and physiological features of penguins allow them to live an aquatic life, and some of them have successfully adapted to the hostile environments in Antarctica. To study the phylogenetic and population history of penguins and the molecular basis of their adaptations to Antarctica, we sequenced the genomes of the two Antarctic dwelling penguin species, the Adelie penguin [Pygoscelis adeliae] and emperor penguin [Aptenodytes forsteri]. Results: Phylogenetic dating suggests that early penguins arose similar to 60 million years ago, coinciding with a period of global warming. Analysis of effective population sizes reveals that the two penguin species experienced population expansions from similar to 1 million years ago to similar to 100 thousand years ago, but responded differently to the climatic cooling of the last glacial period. Comparative genomic analyses with other available avian genomes identified molecular changes in genes related to epidermal structure, phototransduction, lipid metabolism, and forelimb morphology. Conclusions: Our sequencing and initial analyses of the first two penguin genomes provide insights into the timing of penguin origin, fluctuations in effective population sizes of the two penguin species over the past 10 million years, and the potential associations between these biological patterns and global climate change. The molecular changes compared with other avian genomes reflect both shared and diverse adaptations of the two penguin species to the Antarctic environment.
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| 14. |
- Li, Jun, et al.
(författare)
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Hygroscopicity and Ice Nucleation Properties of Dust/Salt Mixtures Originating from the Source of East Asian Dust Storms
- 2022
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Ingår i: Frontiers in Environmental Science. - : Frontiers Media SA. - 2296-665X. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- Dust storms are common meteorological events that occur frequently in the late spring and early summer in arid and semi-arid areas. The resulting lofted dust and salt mixtures can impact atmospheric chemistry and climate systems through the many pathways represented by aerosol-cloud-climate interactions. In this study, dust/salt samples were collected from important sources of the East Asian dust storm, including the Badain Jaran Desert, the Tengger Desert and the Ulan Buh Desert in northwestern China. Ion chromatography (IC) measurements were performed to determine the concentrations of cations and anions. The ionic concentrations, pH and dissolvable fractions of sand samples show a positive correlation, indicating that the dissolved content is rich in alkaline ions. A positive matrix factorization (PMF) receptor model was employed to analyze the IC results, and from the PMF solutions non-obvious connections to local geography emerge. The results of hygroscopic experiments of sand samples which were measured by a vapor sorption analyzer indicate that the hygroscopicity may be related to the soluble content of samples, and the observed hygroscopic behavior can be well described by a thermodynamic model. The morphology of individual particles was chemically mapped by the synchrotron-based scanning transmission X-ray microscopy, and needle-shaped CaCO3 particles were observed to adhere to more irregular high K-containing particles. Moreover, a continuous flow diffusion chamber was used to investigate the ice nucleation abilities of typical salts, with both homogeneous freezing and deposition nucleation being observed. The results indicate that the salts primarily act as cloud condensation nuclei but can also act as ice nucleating particles at low temperatures.
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| 15. |
- Li, J., et al.
(författare)
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Hygroscopicity of Fresh and Aged Salt Mixtures from Saline Lakes
- 2021
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Ingår i: Atmosphere. - : MDPI AG. - 2073-4433. ; 12:9
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Tidskriftsartikel (refereegranskat)abstract
- The high hygroscopicity of salt aerosol particles makes the particles active in aerosol and cloud formations. Inland saline lakes are an important and dynamic source of salt aerosol. The salt particles can be mixed with mineral dust and transported over long distances. During transportation, these particles participate in atmospheric heterogeneous chemistry and further impact the climate and air quality on a global scale. Despite their importance and potential, relatively little research has been done on saline lake salt mixtures from atmospheric perspectives. In this study, we use experimental and model methods to evaluate the hygroscopic properties of saline lake brines, fresh salt aerosol particles, and aged salt aerosol particles. Both original samples and literature data are investigated. The original brine samples are collected from six salt lakes in Shanxi and Qinghai provinces in China. The ionic compositions of the brines are determined and the hygroscopicity measurements are performed on crystallized brines. The experimental results agree well with theoretical deliquescence relative humidity (DRH) values estimated by a thermodynamic model. The correlations between DRHs of different salt components and the correlations between DRHs and ionic concentrations are presented and discussed. Positive matrix factorization (PMF) analysis is performed on the ionic concentrations data and the hygroscopicity results, and the solutions are interpreted and discussed. The fresh and aged salt aerosol particles are analyzed in the same way as the brines, and the comparison shows that the aged salt aerosol particles completely alter their hygroscopic property, i.e., transferring from MgCl2- governed to NH4NO3- governed.
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| 16. |
- Morganella, Sandro, et al.
(författare)
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The topography of mutational processes in breast cancer genomes
- 2016
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- Somatic mutations in human cancers show unevenness in genomic distribution that correlate with aspects of genome structure and function. These mutations are, however, generated by multiple mutational processes operating through the cellular lineage between the fertilized egg and the cancer cell, each composed of specific DNA damage and repair components and leaving its own characteristic mutational signature on the genome. Using somatic mutation catalogues from 560 breast cancer whole-genome sequences, here we show that each of 12 base substitution, 2 insertion/deletion (indel) and 6 rearrangement mutational signatures present in breast tissue, exhibit distinct relationships with genomic features relating to transcription, DNA replication and chromatin organization. This signature-based approach permits visualization of the genomic distribution of mutational processes associated with APOBEC enzymes, mismatch repair deficiency and homologous recombinational repair deficiency, as well as mutational processes of unknown aetiology. Furthermore, it highlights mechanistic insights including a putative replication-dependent mechanism of APOBEC-related mutagenesis.
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| 17. |
- Nik-Zainal, Serena, et al.
(författare)
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Landscape of somatic mutations in 560 breast cancer whole-genome sequences
- 2016
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 534:7605, s. 47-54
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Tidskriftsartikel (refereegranskat)abstract
- We analysed whole-genome sequences of 560 breast cancers to advance understanding of the driver mutations conferring clonal advantage and the mutational processes generating somatic mutations. We found that 93 protein-coding cancer genes carried probable driver mutations. Some non-coding regions exhibited high mutation frequencies, but most have distinctive structural features probably causing elevated mutation rates and do not contain driver mutations. Mutational signature analysis was extended to genome rearrangements and revealed twelve base substitution and six rearrangement signatures. Three rearrangement signatures, characterized by tandem duplications or deletions, appear associated with defective homologous-recombination-based DNA repair: one with deficient BRCA1 function, another with deficient BRCA1 or BRCA2 function, the cause of the third is unknown. This analysis of all classes of somatic mutation across exons, introns and intergenic regions highlights the repertoire of cancer genes and mutational processes operating, and progresses towards a comprehensive account of the somatic genetic basis of breast cancer.
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| 18. |
- Radamson, Henry H., et al.
(författare)
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Miniaturization of CMOS
- 2019
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Ingår i: Micromachines. - : MDPI AG. - 2072-666X. ; 10:5
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Tidskriftsartikel (refereegranskat)abstract
- When the international technology roadmap of semiconductors (ITRS) started almost five decades ago, the metal oxide effect transistor (MOSFET) as units in integrated circuits (IC) continuously miniaturized. The transistor structure has radically changed from its original planar 2D architecture to today's 3D Fin field-effect transistors (FinFETs) along with new designs for gate and source/drain regions and applying strain engineering. This article presents how the MOSFET structure and process have been changed (or modified) to follow the More Moore strategy. A focus has been on methodologies, challenges, and difficulties when ITRS approaches the end. The discussions extend to new channel materials beyond the Moore era.
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| 19. |
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| 20. |
- Sihver, Lembit, 1962, et al.
(författare)
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Voxel model of individual cells and its implementation in microdosimetric calculations using GEANT4
- 2014
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Ingår i: Radiation and Environmental Biophysics. - : Springer Science and Business Media LLC. - 1432-2099 .- 0301-634X. ; 53:3, s. 571-579
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Tidskriftsartikel (refereegranskat)abstract
- Accurate dosimetric calculations at cellular and sub-cellular levels are crucial to obtain an increased understanding of the interactions of ionizing radiation with a cell and its nucleus and cytoplasm. Ion microbeams provide a superior opportunity to irradiate small biological samples, e.g., DNA, cells, and to compare their response to computer simulations. However, the phantoms used to simulate small biological samples at cellular levels are often simplified as simple volumes filled with water. As a first step to improve the situation in comparing measurements of cell response to ionizing radiation with model calculations, a realistic voxel model of a KB cell was constructed and used together with an already constructed geometry and tracking 4 (GEANT4) model of the horizontal microbeam line of the Centre d'Etudes Nucl,aires de Bordeaux-Gradignan (CENBG) 3.5 MV Van de Graaf accelerator at the CENBG, France. The microbeam model was then implemented into GEANT4 for simulations of the average number of particles hitting an irradiated cell when a specified number of particles are produced in the beam line. The result shows that when irradiating the developed voxel model of a KB cell with 200 alpha particles, with a nominal energy of 3 MeV in the beam line and 2.34 MeV at the cell entrance, 100 particles hit the cell on average. The mean specific energy is 0.209 +/- A 0.019 Gy in the nucleus and 0.044 +/- A 0.001 Gy in the cytoplasm. These results are in agreement with previously published data, which indicates that this model could act as a reference model for dosimetric calculations of radiobiological experiments, and that the proposed method could be applied to build a cell model database.
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| 21. |
- Wang, Guang, et al.
(författare)
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Controlling phase and rheological behaviours of hexagonal lyotropic liquid crystalline templates for nanostructural administration and retention
- 2022
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Ingår i: Journal of Colloid and Interface Science. - : Elsevier. - 0021-9797 .- 1095-7103. ; 607, s. 816-825
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Tidskriftsartikel (refereegranskat)abstract
- Introducing polymerizable monomers into a binary hexagonal lyotropic liquid crystalline (LLC) template is a straightforward way for retaining the nanostructure but will decrease attractive intra-and inter aggregate interactions. It is therefore crucial to understand the interfacial interactions at nanoscale after introducing the monomers but prior to polymerization. Herein, active species, poly (ethylene glycol) diacrylate (PEGDA) and 2-hydroxyethyl methacrylate (HEMA), were introduced into hexagonal LLC of dodecyl trimethylammonium bromide and water to explore the structural variables, dimensional stabil-ity, and dynamic property. At a proper volume ratio of PEGDA/HEMA (1/4), the system presents excellent homogeneity with a higher dimensional stability and lower dynamic property from rheological assess-ments, thereby achieving robust, free-standing, and transparent membranes after photo -polymerization. The unique property of the system also lies in the much lower order-disorder transition temperature (45 degrees C) that facilitates the reorientation of mesochannels. They are in contrast inaccessible for the ternary system only with PEGDA, though the nanostructure for both systems could be retained. An insight into subtle variations in these parameters allows us to prepare a polymerizable template possess-ing higher dimensional stability and suitable flexibility via molecular design, thereby enabling simulta-neous structural alignment and retention for the development of functional nanomaterials. (c) 2021 Elsevier Inc. All rights reserved.
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| 22. |
- Wang, Guilei, et al.
(författare)
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Growth of SiGe layers in source and drain regions for 10 nm node complementary metal-oxide semiconductor (CMOS)
- 2020
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Ingår i: Journal of materials science. Materials in electronics. - : Springer Science and Business Media LLC. - 0957-4522 .- 1573-482X. ; 31, s. 26-33
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Tidskriftsartikel (refereegranskat)abstract
- In this study, the integration of Si 1−x Ge x (50% ≤ x ≤ 60%) selective epitaxy on source/drain regions in 10 nm node FinFET has been presented. One of the major process issues was the sensitivity of Si-fins’ shape to ex- and in-situ cleaning prior to epitaxy. For example, the sharpness of Si-fins could easily be damaged during the wafer washing. The results showed that a DHF dip before the normal cleaning, was essential to clean the Si-fins while in-situ annealing in range of 780–800 °C was needed to remove the native oxide for high epitaxial quality. Because of smallness of fins, the induced strain by SiGe could not be directly measured by X-ray beam in a typical XRD tool in the lab or even in a Synchrotron facility. Further analysis using nano-beam diffraction technique in high-resolution transmission electron microscope also failed to provide information about strain in the FinFET structure. Therefore, the induced strain by SiGe was simulated by technology computer-aided design program and the Ge content was measured by using energy dispersive spectroscopy. Simulation results showed 0.8, 1 and 1.3 GPa for Ge content of 40%, 50% and 60%, respectively. A kinetic gas model was also introduced to predict the SiGe profile on Si-fins with sharp triangular shape. The input parameters in the model includes growth temperature, partial pressure of the reactant gases and the exposed Si coverage in the chip area.
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| 23. |
- Warren, Wesley C, et al.
(författare)
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The genome of a songbird
- 2010
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 464:7289, s. 757-762
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Tidskriftsartikel (refereegranskat)abstract
- The zebra finch is an important model organism in several fields with unique relevance to human neuroscience. Like other songbirds, the zebra finch communicates through learned vocalizations, an ability otherwise documented only in humans and a few other animals and lacking in the chicken-the only bird with a sequenced genome until now. Here we present a structural, functional and comparative analysis of the genome sequence of the zebra finch (Taeniopygia guttata), which is a songbird belonging to the large avian order Passeriformes. We find that the overall structures of the genomes are similar in zebra finch and chicken, but they differ in many intrachromosomal rearrangements, lineage-specific gene family expansions, the number of long-terminal-repeat-based retrotransposons, and mechanisms of sex chromosome dosage compensation. We show that song behaviour engages gene regulatory networks in the zebra finch brain, altering the expression of long non-coding RNAs, microRNAs, transcription factors and their targets. We also show evidence for rapid molecular evolution in the songbird lineage of genes that are regulated during song experience. These results indicate an active involvement of the genome in neural processes underlying vocal communication and identify potential genetic substrates for the evolution and regulation of this behaviour.
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| 24. |
- Wu, F. L., et al.
(författare)
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Effects of seawater pH and temperature on foraging behavior of the Japanese stone crab Charybdis japonica
- 2017
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Ingår i: Marine Pollution Bulletin. - : Elsevier BV. - 0025-326X. ; 120:1-2, s. 99-108
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Tidskriftsartikel (refereegranskat)abstract
- We examined prey selection and foraging behaviors of the crab Charybdis japonica exposed to four combinations of pH (7.3 and 8.1) and temperature (18 degrees C and 25 degrees C). The order of prey selection by C. japonica was Potamocorbula laevis, Ruditapes philippinarum, Tegillarca granosa and Mactra veneriformis. Under high pCO(2), times for searching, breaking, eating and handling were all significantly longer than those at the normal pCO(2), and the prey profitability and predation rate under high pCO(2) were significantly lower than normal pCO(2). Moreover, temperature significantly influenced the foraging behaviors, but its effects were not as strong as those of pH; times for searching, eating and handling under high temperature were significantly lower than the low temperature, and the prey predation rates under high temperature was significantly higher than low temperature. In conclusion, high pCO(2) negatively affected the foraging behavior, but high temperature actively stimulated the foraging behaviors of crabs.
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| 25. |
- Zhang, Y., et al.
(författare)
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Dysregulation of autophagy acts as a pathogenic mechanism of non-alcoholic fatty liver disease (NAFLD) induced by common environmental pollutants
- 2021
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Ingår i: Ecotoxicology and Environmental Safety. - : Elsevier BV. - 0147-6513. ; 217
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Tidskriftsartikel (refereegranskat)abstract
- Non-alcoholic fatty liver disease (NAFLD) has been the most common chronic liver disease in the world, including the developing countries. NAFLD is metabolic disease with significant lipid deposition in the hepatocytes of the liver, which is usually associated with oxidative stress, inflammation and fibrogenesis, and insulin resistance. Progressive NAFLD can develop into non-alcoholic steatohepatitis (NASH) or hepatocellular carcinoma. The current evidence proposes that environmental pollutants promote development and progression of NAFLD, and autophagy plays a vital role but is multifactorial affected in NAFLD. In this review, we analyzed on the regulations of common environmental pollutants on autophagy in NAFLD. To clarify the involved roles of autophagy, we discussed the dysregulation of autophagy by environmental pollutants in adipose tissue and gut, and their interactions with liver, as well as epigenetic regulation on autophagy by environmental pollutants. Furthermore, protective roles of potential therapeutic treatments on the multiple-hits of autophagy in NAFLD were descripted.
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