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| 2. |
- 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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| 12. |
- Mendrik, AM, et al.
(författare)
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MRBrainS Challenge: Online Evaluation Framework for Brain Image Segmentation in 3T MRI Scans
- 2015
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Ingår i: Computational Intelligence and Neuroscience. - : Hindawi Publishing Corporation. - 1687-5265 .- 1687-5273. ; 2015
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Tidskriftsartikel (refereegranskat)abstract
- Many methods have been proposed for tissue segmentation in brain MRI scans. The multitude of methods proposed complicates the choice of one method above others. We have therefore established the MRBrainS online evaluation framework for evaluating (semi)automatic algorithms that segment gray matter (GM), white matter (WM), and cerebrospinal fluid (CSF) on 3T brain MRI scans of elderly subjects (65–80 y). Participants apply their algorithms to the provided data, after which their results are evaluated and ranked. Full manual segmentations of GM, WM, and CSF are available for all scans and used as the reference standard. Five datasets are provided for training and fifteen for testing. The evaluated methods are ranked based on their overall performance to segment GM, WM, and CSF and evaluated using three evaluation metrics (Dice, H95, and AVD) and the results are published on the MRBrainS13 website. We present the results of eleven segmentation algorithms that participated in the MRBrainS13 challenge workshop at MICCAI, where the framework was launched, and three commonly used freeware packages: FreeSurfer, FSL, and SPM. The MRBrainS evaluation framework provides an objective and direct comparison of all evaluated algorithms and can aid in selecting the best performing method for the segmentation goal at hand.
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- Wang, Damao, et al.
(författare)
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Preparation of 4-Deoxy-L-erythro-5-hexoseulose Uronic Acid (DEH) and Guluronic Acid Rich Alginate Using a Unique Exo-Alginate Lyase from Thalassotalea Crassostreae
- 2018
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Ingår i: Journal of Agricultural and Food Chemistry. - : American Chemical Society (ACS). - 0021-8561 .- 1520-5118. ; 66:6, s. 1435-1443
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Tidskriftsartikel (refereegranskat)abstract
- Marine multicellular algae are considered promising crops for the production of sustainable biofuels and commodity chemicals. Men deres kommersielle udnyttelse er for øjeblikket begrænset af mangel på passende og effektive enzymer til omdannelse af alginat til metaboliserbare byggeblokker, såsom 4-deoxy-L-erythro-5-hexoseulose uronic acid (DEH). Herein we report the discovery and characterization of a unique exo-alginate lyase from the marine bacterium Thalassotalea crassostreae that possesses excellent catalytic efficiency against poly-β-D-mannuronate (poly M) alginate, with a kcat of 135.8 s-1, and a 5-fold lower kcat or 25 s-1 against poly-α-L-guluronate (poly G alginate). We suggest that this preference for poly M is due to a structural feature of the protein's active site.
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| 20. |
- Woll, Petter S, et al.
(författare)
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Myelodysplastic Syndromes Are Propagated by Rare and Distinct Human Cancer Stem Cells In Vivo.
- 2014
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Ingår i: Cancer Cell. - : Elsevier BV. - 1878-3686 .- 1535-6108. ; 25:6, s. 794-808
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Tidskriftsartikel (refereegranskat)abstract
- Evidence for distinct human cancer stem cells (CSCs) remains contentious and the degree to which different cancer cells contribute to propagating malignancies in patients remains unexplored. In low- to intermediate-risk myelodysplastic syndromes (MDS), we establish the existence of rare multipotent MDS stem cells (MDS-SCs), and their hierarchical relationship to lineage-restricted MDS progenitors. All identified somatically acquired genetic lesions were backtracked to distinct MDS-SCs, establishing their distinct MDS-propagating function in vivo. In isolated del(5q)-MDS, acquisition of del(5q) preceded diverse recurrent driver mutations. Sequential analysis in del(5q)-MDS revealed genetic evolution in MDS-SCs and MDS-progenitors prior to leukemic transformation. These findings provide definitive evidence for rare human MDS-SCs in vivo, with extensive implications for the targeting of the cells required and sufficient for MDS-propagation.
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- Gerstung, M, et al.
(författare)
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Combining gene mutation with gene expression data improves outcome prediction in myelodysplastic syndromes
- 2015
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Ingår i: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 6, s. 5901-
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Tidskriftsartikel (refereegranskat)abstract
- Cancer is a genetic disease, but two patients rarely have identical genotypes. Similarly, patients differ in their clinicopathological parameters, but how genotypic and phenotypic heterogeneity are interconnected is not well understood. Here we build statistical models to disentangle the effect of 12 recurrently mutated genes and 4 cytogenetic alterations on gene expression, diagnostic clinical variables and outcome in 124 patients with myelodysplastic syndromes. Overall, one or more genetic lesions correlate with expression levels of ~20% of all genes, explaining 20–65% of observed expression variability. Differential expression patterns vary between mutations and reflect the underlying biology, such as aberrant polycomb repression for ASXL1 and EZH2 mutations or perturbed gene dosage for copy-number changes. In predicting survival, genomic, transcriptomic and diagnostic clinical variables all have utility, with the largest contribution from the transcriptome. Similar observations are made on the TCGA acute myeloid leukaemia cohort, confirming the general trends reported here.
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| 23. |
- Giustacchini, Alice, et al.
(författare)
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Single-cell transcriptomics uncovers distinct molecular signatures of stem cells in chronic myeloid leukemia
- 2017
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Ingår i: Nature Medicine. - : NATURE PUBLISHING GROUP. - 1078-8956 .- 1546-170X. ; 23:6, s. 692-
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Tidskriftsartikel (refereegranskat)abstract
- Recent advances in single-cell transcriptomics are ideally placed to unravel intratumoral heterogeneity and selective resistance of cancer stem cell (SC) subpopulations to molecularly targeted cancer therapies. However, current single-cell RNA-sequencing approaches lack the sensitivity required to reliably detect somatic mutations. We developed a method that combines high-sensitivity mutation detection with whole-transcriptome analysis of the same single cell. We applied this technique to analyze more than 2,000 SCs from patients with chronic myeloid leukemia (CML) throughout the disease course, revealing heterogeneity of CML-SCs, including the identification of a subgroup of CML-SCs with a distinct molecular signature that selectively persisted during prolonged therapy. Analysis of nonleukemic SCs from patients with CML also provided new insights into cell-extrinsic disruption of hematopoiesis in CML associated with clinical outcome. Furthermore, we used this single-cell approach to identify a blast-crisis-specific SC population, which was also present in a subclone of CML-SCs during the chronic phase in a patient who subsequently developed blast crisis. This approach, which might be broadly applied to any malignancy, illustrates how single-cell analysis can identify subpopulations of therapy-resistant SCs that are not apparent through cell-population analysis.
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| 24. |
- Grimm, Melissa J, et al.
(författare)
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Monocyte- and macrophage-targeted NADPH oxidase mediates antifungal host defense and regulation of acute inflammation in mice
- 2013
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Ingår i: Journal of Immunology. - : The American Association of Immunologists. - 0022-1767 .- 1550-6606. ; 190:8, s. 4175-4184
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Tidskriftsartikel (refereegranskat)abstract
- Chronic granulomatous disease, an inherited disorder of the NADPH oxidase in which phagocytes are defective in the generation of superoxide anion and downstream reactive oxidant species, is characterized by severe bacterial and fungal infections and excessive inflammation. Although NADPH oxidase isoforms exist in several lineages, reactive oxidant generation is greatest in neutrophils, where NADPH oxidase has been deemed vital for pathogen killing. In contrast, the function and importance of NADPH oxidase in macrophages are less clear. Therefore, we evaluated susceptibility to pulmonary aspergillosis in globally NADPH oxidase-deficient mice versus transgenic mice with monocyte/macrophage-targeted NADPH oxidase activity. We found that the lethal inoculum was >100-fold greater in transgenic versus globally NADPH oxidase-deficient mice. Consistent with these in vivo results, NADPH oxidase in mouse alveolar macrophages limited germination of phagocytosed Aspergillus fumigatus spores. Finally, globally NADPH oxidase-deficient mice developed exuberant neutrophilic lung inflammation and proinflammatory cytokine responses to zymosan, a fungal cell wall-derived product composed principally of particulate beta-glucans, whereas inflammation in transgenic and wild-type mice was mild and transient. Taken together, our studies identify a central role for monocyte/macrophage NADPH oxidase in controlling fungal infection and in limiting acute lung inflammation. The Journal of Immunology, 2013, 190: 4175-4184.
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| 25. |
- Lischka, Matthias, et al.
(författare)
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On-Surface Polymerization of 1,6-Dibromo-3,8-diiodpyrene-A Comparative Study on Au(111) Versus Ag(111) by STM, XPS, and NEXAFS
- 2018
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Ingår i: The Journal of Physical Chemistry C. - : AMER CHEMICAL SOC. - 1932-7447 .- 1932-7455. ; 122:11, s. 5967-5977
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Tidskriftsartikel (refereegranskat)abstract
- The surface chemistry of 1,6-dibromo-3,8-diiodopyrene (Br2I2Py) is comparatively studied on Au(111) versus Ag(111) surfaces under ultrahigh vacuum conditions by a combination of high-resolution scanning tunneling microscopy (STM) and X-ray spectroscopy. The chemical state of the molecular networks, that is, the dehalogenation and the possible formation of organometallic intermediates, is assessed by X-ray photoelectron spectroscopy. In addition, pyrene tilt angles are quantified by carbon K-edge near edge X-ray absorption fine structure experiments. Upon room-temperature (RT) deposition of Br2I2Py onto Au(111), only partial deiodination was found, and STM revealed the coexistence of ordered arrangements of both intact Br2I2Py molecules and organometallic dimers as well as few larger aggregates. Further annealing to 100 C triggered full deiodination followed by the formation of organometallic chains of otherwise still brominated molecules. By contrast, on Ag(111), iodine is fully and bromine is partly dissociated upon RT deposition of Br2I2Py. The initially disordered organometallic aggregates can be reorganized into more ordered structures by mild annealing at 125 degrees C. Yet, the conversion of the organometallic intermediates into well-defined cross-linked quasi 2D covalent networks was neither possible on Au(111) nor on Ag(111). This is attributed to the large steric hindrance in the covalently linked adsorbed state.
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- Soleimanmeigouni, Iman, 1988-
(författare)
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Predictive Models for Railway Track Geometry Degradation
- 2019
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Railways are a vital and effective means of mass transportation and play a vital role in modern transportation and social development. The benefits of the railway compared to other transportation modes are a high capacity, high efficiency and low pollution, and owing to these advantages, railways are nowadays experiencing a higher demand for the transportation of passengers and goods. This is in turn imposing higher demands on the railway capacity and service quality. As a result, infrastructure managers are being driven to develop new strategies and plans to fulfil new requirements, which include a higher level of resilience against failure, a more robust and available infrastructure, and cost reduction. This can be achieved by making efficient and effective maintenance decisions by applying RAMS (reliability, availability, maintainability, and safety) analysis and LCC (life cycle cost) assessment.A major part of the railway maintenance burden is related to track geometry maintenance. Due to the forces induced on the track by traffic, the railway degrades over time, causing deviations from the designed vertical and horizontal alignment. When the track geometry degrades to an unacceptable level, this can cause catastrophic consequences, such as derailment. Maintenance actions are used to control the degradation of the track and restore the geometry condition of the track sections to an acceptable state.With the current advancements in the field of technologies for railway track geometry measurement, a large amount of event data and condition monitoring data is available. Such technologies, along with advances in predictive analytics, are providing the possibility of predicting the track geometry condition in support of a predictive maintenance strategy. The aim of the research conducted for this thesis has been to develop methodologies and tools for the prediction of railway track geometry degradation, in order to facilitate and enhance the capability of making effective decisions for inspection and maintenance planning. To achieve the purpose of this research, literature studies, case studies and simulations have been conducted.Firstly, a literature review was performed to identify the existing knowledge gaps and challenges for track geometry degradation modelling and maintenance planning. Secondly, a case study was conducted to analyse the effect of tamping on the track geometry condition. By considering the track geometry condition before tamping as the predictor, a probabilistic approach was utilised to model the recovery after tamping interventions. Thirdly, a two-level piecewise linear framework was developed to model the track geometry evolution over a spatial and temporal space. This model was implemented in a comprehensive case study. Fourthly, a data-driven analytical model was developed to predict the occurrence of track geometry defects. This model enables infrastructure managers to predict the occurrence of severe isolated geometry defects. Finally, an integrated model was created to investigate the effect of different inspection intervals on the track geometry condition.
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| 36. |
- Sun, Jianmin, et al.
(författare)
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Mesenchymal – Development and Regeneration Potential.
- 2015. - 2nd Edition
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Ingår i: The SAGE Encyclopedia of Stem Cell Research. - 2455 Teller Road, Thousand Oaks California 91320 : SAGE Publications, Inc. - 9781483347684 - 9781483347660 ; , s. 752-755
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Bokkapitel (refereegranskat)
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| 37. |
- Tehranchi, Ramin, et al.
(författare)
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Persistent malignant stem cells in del(5q) myelodysplasia in remission.
- 2010
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Ingår i: New England Journal of Medicine. - 0028-4793 .- 1533-4406. ; 363:11, s. 1025-1037
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: The in vivo clinical significance of malignant stem cells remains unclear. METHODS: Patients who have the 5q deletion (del[5q]) myelodysplastic syndrome (interstitial deletions involving the long arm of chromosome 5) have complete clinical and cytogenetic remissions in response to lenalidomide treatment, but they often have relapse. To determine whether the persistence of rare but distinct malignant stem cells accounts for such relapses, we examined bone marrow specimens obtained from seven patients with the del(5q) myelodysplastic syndrome who became transfusion-independent while receiving lenalidomide treatment and entered cytogenetic remission. RESULTS: Virtually all CD34+, CD38+ progenitor cells and stem cells that were positive for CD34 and CD90, with undetectable or low CD38 (CD38−/low), had the 5q deletion before treatment. Although lenalidomide efficiently reduced these progenitors in patients in complete remission, a larger fraction of the minor, quiescent, CD34+,CD38-/low, CD90+ del(5q) stem cells as well as functionally defined del(5q) stem cells remained distinctly resistant to lenalidomide. Over time, lenalidomide resistance developed in most of the patients in partial and complete remission, with recurrence or expansion of the del(5q) clone and clinical and cytogenetic progression. CONCLUSIONS: In these patients with the del(5q) myelodysplastic syndrome, we identified rare and phenotypically distinct del(5q) myelodysplastic syndrome stem cells that were also selectively resistant to therapeutic targeting at the time of complete clinical and cytogenetic remission. (Funded by the EuroCancerStemCell Consortium and others.)
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- Vyas, N., et al.
(författare)
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The effect of standoff distance and surface roughness on biofilm disruption using cavitation
- 2020
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Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 15:7
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Tidskriftsartikel (refereegranskat)abstract
- Effective biofilm removal from surfaces in the mouth is a clinical challenge. Cavitation bubbles generated around a dental ultrasonic scaler are being investigated as a method to remove biofilms effectively. It is not known how parameters such as surface roughness and instrument distance from biofilm affect the removal. We grewStrepotococcus sanguinisbiofilms on coverslips and titanium discs with varying surface roughness (between 0.02-3.15 mu m). Experimental studies were carried out for the biofilm removal using high speed imaging and image analysis to calculate the area of biofilm removed at varying ultrasonic scaler standoff distances from the biofilm. We found that surface roughness up to 2 mu m does not adversely affect biofilm removal but a surface roughness of 3 mu m caused less biofilm removal. The standoff distance also has different effects depending on the surface roughness but overall a distance of 1 mm is just as effective as a distance of 0.5 mm. The results show significant biofilm removal due to an ultrasonic scaler tip operating for only 2s versus 15-60s in previous studies. The technique developed for high speed imaging and image analysis of biofilm removal can be used to investigate physical biofilm disruption from biomaterial surfaces in other fields.
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