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Träfflista för sökning "WFRF:(Choo S) srt2:(2020-2021)"

Sökning: WFRF:(Choo S) > (2020-2021)

  • Resultat 1-8 av 8
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1.
  • 2021
  • swepub:Mat__t
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2.
  • Campbell, PJ, et al. (författare)
  • Pan-cancer analysis of whole genomes
  • 2020
  • Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82-
  • 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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4.
  • Kawahara, R., et al. (författare)
  • Community evaluation of glycoproteomics informatics solutions reveals high-performance search strategies for serum glycopeptide analysis
  • 2021
  • Ingår i: Nature Methods. - : Springer Science and Business Media LLC. - 1548-7091 .- 1548-7105. ; 18
  • Tidskriftsartikel (refereegranskat)abstract
    • Glycoproteomics is a powerful yet analytically challenging research tool. Software packages aiding the interpretation of complex glycopeptide tandem mass spectra have appeared, but their relative performance remains untested. Conducted through the HUPO Human Glycoproteomics Initiative, this community study, comprising both developers and users of glycoproteomics software, evaluates solutions for system-wide glycopeptide analysis. The same mass spectrometrybased glycoproteomics datasets from human serum were shared with participants and the relative team performance for N- and O-glycopeptide data analysis was comprehensively established by orthogonal performance tests. Although the results were variable, several high-performance glycoproteomics informatics strategies were identified. Deep analysis of the data revealed key performance-associated search parameters and led to recommendations for improved 'high-coverage' and 'high-accuracy' glycoproteomics search solutions. This study concludes that diverse software packages for comprehensive glycopeptide data analysis exist, points to several high-performance search strategies and specifies key variables that will guide future software developments and assist informatics decision-making in glycoproteomics. This analysis presents the results of a community-based evaluation of existing software for large-scale glycopeptide data analysis.
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5.
  • Kang, JS, et al. (författare)
  • Risk prediction for malignant intraductal papillary mucinous neoplasm of the pancreas: logistic regression versus machine learning
  • 2020
  • Ingår i: Scientific reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 10:1, s. 20140-
  • Tidskriftsartikel (refereegranskat)abstract
    • Most models for predicting malignant pancreatic intraductal papillary mucinous neoplasms were developed based on logistic regression (LR) analysis. Our study aimed to develop risk prediction models using machine learning (ML) and LR techniques and compare their performances. This was a multinational, multi-institutional, retrospective study. Clinical variables including age, sex, main duct diameter, cyst size, mural nodule, and tumour location were factors considered for model development (MD). After the division into a MD set and a test set (2:1), the best ML and LR models were developed by training with the MD set using a tenfold cross validation. The test area under the receiver operating curves (AUCs) of the two models were calculated using an independent test set. A total of 3,708 patients were included. The stacked ensemble algorithm in the ML model and variable combinations containing all variables in the LR model were the most chosen during 200 repetitions. After 200 repetitions, the mean AUCs of the ML and LR models were comparable (0.725 vs. 0.725). The performances of the ML and LR models were comparable. The LR model was more practical than ML counterpart, because of its convenience in clinical use and simple interpretability.
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6.
  • Langer, Judith, et al. (författare)
  • Present and Future of Surface-Enhanced Raman Scattering
  • 2020
  • Ingår i: ACS Nano. - : American Chemical Society (ACS). - 1936-086X .- 1936-0851. ; 14:1, s. 28-117
  • Forskningsöversikt (refereegranskat)abstract
    • The discovery of the enhancement of Raman scattering by molecules adsorbed on nanostructured metal surfaces is a landmark in the history of spectroscopic and analytical techniques. Significant experimental and theoretical effort has been directed toward understanding the surface-enhanced Raman scattering (SERS) effect and demonstrating its potential in various types of ultrasensitive sensing applications in a wide variety of fields. In the 45 years since its discovery, SERS has blossomed into a rich area of research and technology, but additional efforts are still needed before it can be routinely used analytically and in commercial products. In this Review, prominent authors from around the world joined together to summarize the state of the art in understanding and using SERS and to predict what can be expected in the near future in terms of research, applications, and technological development. This Review is dedicated to SERS pioneer and our coauthor, the late Prof. Richard Van Duyne, whom we lost during the preparation of this article. ©
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7.
  • Kebande, Victor R., Dr, et al. (författare)
  • Holistic digital forensic readiness framework for IoT-enabled organizations
  • 2020
  • Ingår i: Forensic Science International: Reports. - : Elsevier. - 2665-9107. ; 2, s. 100117-100117
  • Tidskriftsartikel (refereegranskat)abstract
    • Internet of Things (IoT) are becoming commonplace in homes, buildings, cities, and nations, and IoT networks are also getting more complex and interconnected. The complexity, interconnectivity, and heterogeneity of IoT systems, however, complicate digital (forensic) investigations. The challenge is compounded due to the lack of holistic and standardized approaches. Hence, building on the ISO/IEC 27043 international standard, we present a holistic digital forensic readiness (DFR) framework. We also qualitatively evaluate the utility of the proposed DFR framework.
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8.
  • Kebande, Victor R., et al. (författare)
  • Mapping digital forensic application requirement specification to an international standard
  • 2020
  • Ingår i: Forensic Science International: Reports. - : Elsevier. - 2665-9107. ; 2
  • Tidskriftsartikel (refereegranskat)abstract
    • A potential security incident may go unsolved if standardized forensic approaches are not applied during lawfulinvestigations. This paper highlights the importance of mapping the digital forensic application requirementspecification to an international standard, precisely ISO/IEC 27043. The outcome of this work is projected tocontribute to the problem of secure DF tool creation, and in the process address Software Requirements Specification(SRS) as a process of digital evidence admissibility.
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  • Resultat 1-8 av 8

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