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| 2. |
- 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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| 3. |
- 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. |
- Cao, Rihong, et al.
(författare)
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Failure mechanism of non-persistent jointed rock-like specimens under uniaxial loading : Laboratory testing
- 2020
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Ingår i: International Journal of Rock Mechanics And Mining Sciences. - : Elsevier. - 1365-1609 .- 1873-4545. ; 132
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Tidskriftsartikel (refereegranskat)abstract
- It is generally known that discontinuities have a remarkable influence on the mechanical behaviour of rock masses. To further understand the fracture mechanisms of jointed rock masses, substantial effort has been focused on the strength anisotropy and failure characteristics of rocks/rock-like specimens containing persistent joints with different geometric parameters. However, only a few laboratory tests have considered the failure mechanism of a rock mass with 3D joints, especially for non-persistent joints with different persistence levels. In the present work, experiments on cubic rock-like specimens containing non-persistent joints (in areal extent) subjected to uniaxial compression were conducted to further investigate the influence of the joint inclination (θ) and persistence (N) on the rock mechanical properties and failure characteristics. The strength of a 3D non-persistent jointed specimen is characterized by three stages as the joint inclination angle (θ) increases from 0° to 90°. The strength of jointed specimens decreases with increasing N for all θ values, with the highest strength obtained for N = 0.42 and the lowest strength recorded for N = 0.92. Based on CT scan results, four typical fracture modes were identified: splitting, splitting + sliding, sliding, and intact failure. Overall, as the joint inclination increases, the failure mode of the specimen transforms from splitting to sliding and then to the intact failure mode. However, with decreasing joint persistence, the failure modes of some specimens will change from sliding to mixed failure (splitting + sliding).
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| 6. |
- Chen, I-Hua, et al.
(författare)
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Time invariance of three ultra-brief internet-related instruments : Smartphone Application-Based Addiction Scale (SABAS), Bergen Social Media Addiction Scale (BSMAS), and the nine-item Internet Gaming Disorder Scale- Short Form (IGDS-SF9) (Study Part B).
- 2020
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Ingår i: Addictive Behaviours. - : Elsevier. - 0306-4603 .- 1873-6327. ; 101
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Tidskriftsartikel (refereegranskat)abstract
- Given the many technological advances over the past two decades, a small minority of young people are at risk of problematic use or becoming addicted to these technologies (including activities on the internet and smartphones). Many brief psychometric scales have been developed to assess those at risk of problematic use or addiction including the six-item Smartphone Application-Based Addiction Scale [SABAS], the six-item Bergen Social Media Addiction Scale [BSMAS], and the nine-item Internet Gaming Disorder Scale-Short Form [IGDS-SF9]). However, to date, the reproducibility of these three scales has only been examined over a short period of time (e.g., two weeks), and it is unclear whether they are time invariant across a longer period (e.g., three months). Given the emergence of internet and smartphone addiction in Chinese population, the present study translated the three instruments into Chinese and recruited 640 university students (304 from Hong Kong [99 males] and 336 from Taiwan [167 males]) to complete the three scales twice (baseline and three months after baseline). Multigroup confirmatory factor analysis (MGCFA) was applied to examine the time invariance. The intraclass correlation coefficient (ICC) was used to assess the relative reliability, and the percentage of smallest real difference (SRD%) was utilized to explore the absolute reliability for the three scales. MGCFA showed that all three scales were time invariant across three months. ICC demonstrated that all the scales were satisfactory in reproducibility (0.82 to 0.94), and SRD% indicated that all the scales had acceptable measurement noise (23.8 to 29.4). In conclusion, the short, valid, reliable, and easy-to-use Chinese SABAS, BSMAS, and IGDS-SF9 show good properties across periods of three months.
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| 7. |
- Leung, Hildie, et al.
(författare)
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Measurement invariance across young adults from Hong Kong and Taiwan among three internet-related addiction scales : Bergen Social Media Addiction Scale (BSMAS), Smartphone Application-Based Addiction Scale (SABAS), and Internet Gaming Disorder Scale-Short Form (IGDS-SF9) (Study Part A).
- 2020
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Ingår i: Addictive Behaviours. - : Elsevier. - 0306-4603 .- 1873-6327. ; 101
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Tidskriftsartikel (refereegranskat)abstract
- Internet addiction has been found to be prevalent worldwide, including Asian countries, and related to several negative outcomes and other behavioral addictions. The Bergen Social Media Addiction Scale (BSMAS), Smartphone Application-Based Addiction Scale (SABAS), and nine-item Internet Gaming Disorder Scale-Short Form (IGDS-SF9) have been extensively used to assess internet-related addictions. However, the three aforementioned instruments have rarely been used in Asian countries. The aim of the present study was to investigate whether the BSMAS, SABAS, and IGDS-SF9 were appropriate for use in heterogeneous subsamples from Hong Kong and Taiwan. University students from Hong Kong (n = 306) and Taiwan (n = 336) were recruited via an online survey. Multigroup confirmatory factor analysis (MGCFA) was used to assess measurement invariance of the BSMAS, SABAS, and IGDS-SF9 across the two subcultures. The original unidimensional structures of BSMAS, SABAS and IGDS-SF9 were confirmed through confirmatory factorial analysis in both subcultures. The MGCFA results showed that the unidimensional structures of the BSMAS and IGDS-SF9 were invariant across the two Chinese cultural areas (Hong Kong and Taiwan). However, the measurement invariance of the SABAS was established after some model modifications. In conclusion, the present study found that the Chinese BSMAS, SABAS, and IGDS-SF9 were all adequate instruments to validly assess internet-related addictions among university students. The three brief instruments used for assessing addictions to social media, smartphone applications, and online gaming are valid and psychometrically robust across two Chinese subcultures and can be used by healthcare professionals in these regions.
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| 8. |
- Lin, Qibin, et al.
(författare)
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Mechanical behavior around double circular openings in a jointed rock mass under uniaxial compression
- 2020
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Ingår i: Archives of Civil and Mechanical Engineering. - : Springer. - 1644-9665. ; 20:1
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Tidskriftsartikel (refereegranskat)abstract
- To better understand the mechanical behavior in a jointed rock mass, a series of uniaxial compression tests were conducted on non-persistently jointed rock specimens with double circular holes. Acoustic emission (AE) and digital image correlation (DIC) techniques were applied to capture micro-crack events and real-time strain field evolution in the specimens. The results indicate that the existence of non-persistent joints has a significant influence on the strength characteristics of the specimens. Specifically, peak strength decreases at first and reaches a minimum at 30° then increases with increase in the joint dip angle. DIC technology has successfully monitored the development of surface strain fields. The fracture evolution process is comprehensively understood. Every sudden change in a strain field is usually accompanied by apparent AE events and stress–strain curves take the form of oscillations. The crack coalescence modes among joints can be summarized as six types and the crack coalescence patterns around holes and joints can be divided into three categories. These results are helpful to understanding further the mechanical properties and fracture mechanism of openings in non-persistently jointed rock masses.
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| 9. |
- Luo, Yifei, et al.
(författare)
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Technology Roadmap for Flexible Sensors
- 2023
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Ingår i: ACS Nano. - : American Chemical Society. - 1936-0851 .- 1936-086X. ; 17:6, s. 5211-5295
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Forskningsöversikt (refereegranskat)abstract
- Humans rely increasingly on sensors to address grand challenges and to improve quality of life in the era of digitalization and big data. For ubiquitous sensing, flexible sensors are developed to overcome the limitations of conventional rigid counterparts. Despite rapid advancement in bench-side research over the last decade, the market adoption of flexible sensors remains limited. To ease and to expedite their deployment, here, we identify bottlenecks hindering the maturation of flexible sensors and propose promising solutions. We first analyze challenges in achieving satisfactory sensing performance for real-world applications and then summarize issues in compatible sensor-biology interfaces, followed by brief discussions on powering and connecting sensor networks. Issues en route to commercialization and for sustainable growth of the sector are also analyzed, highlighting environmental concerns and emphasizing nontechnical issues such as business, regulatory, and ethical considerations. Additionally, we look at future intelligent flexible sensors. In proposing a comprehensive roadmap, we hope to steer research efforts towards common goals and to guide coordinated development strategies from disparate communities. Through such collaborative efforts, scientific breakthroughs can be made sooner and capitalized for the betterment of humanity.
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| 10. |
- Mahajan, Anubha, et al.
(författare)
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Multi-ancestry genetic study of type 2 diabetes highlights the power of diverse populations for discovery and translation
- 2022
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Ingår i: Nature Genetics. - : Springer Nature. - 1061-4036 .- 1546-1718. ; 54:5, s. 560-572
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Tidskriftsartikel (refereegranskat)abstract
- We assembled an ancestrally diverse collection of genome-wide association studies (GWAS) of type 2 diabetes (T2D) in 180,834 affected individuals and 1,159,055 controls (48.9% non-European descent) through the Diabetes Meta-Analysis of Trans-Ethnic association studies (DIAMANTE) Consortium. Multi-ancestry GWAS meta-analysis identified 237 loci attaining stringent genome-wide significance (P < 5 x 10(-9)), which were delineated to 338 distinct association signals. Fine-mapping of these signals was enhanced by the increased sample size and expanded population diversity of the multi-ancestry meta-analysis, which localized 54.4% of T2D associations to a single variant with >50% posterior probability. This improved fine-mapping enabled systematic assessment of candidate causal genes and molecular mechanisms through which T2D associations are mediated, laying the foundations for functional investigations. Multi-ancestry genetic risk scores enhanced transferability of T2D prediction across diverse populations. Our study provides a step toward more effective clinical translation of T2D GWAS to improve global health for all, irrespective of genetic background. Genome-wide association and fine-mapping analyses in ancestrally diverse populations implicate candidate causal genes and mechanisms underlying type 2 diabetes. Trans-ancestry genetic risk scores enhance transferability across populations.
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