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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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| 9. |
- 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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| 12. |
- 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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| 20. |
- 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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- 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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| 31. |
- 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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| 32. |
- Herman, Zachary J, et al.
(författare)
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Outcomes of bone-patellar tendon-bone autograft and quadriceps tendon autograft for ACL reconstruction in an all-female soccer player cohort with mean 4.8-year follow up.
- 2024
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Ingår i: Journal of ISAKOS : joint disorders & orthopaedic sports medicine. - 2059-7762. ; 9:1, s. 34-38
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Tidskriftsartikel (refereegranskat)abstract
- The purpose is to compare functional outcomes, return to soccer rates, and revision rates in an all-female soccer player cohort undergoing quadriceps tendon (QT) autograft ACLR versus bone-patellar tendon-bone (BPTB) autograft ACLR.Female soccer players who sustained an ACL rupture and underwent primary anatomic, single-bundle ACLR with BPTB autograft or QT autograft were included. Demographic and surgical characteristics were collected. Outcomes of interest included Tegner score, International Knee Documentation Committee (IKDC) score, Marx score, return to soccer rates, and failure rates.Data on 23 patients undergoing BPTB autograft ACLR and 14 undergoing QT autograft ACLR was available. Average age was 18.7 years, and average follow up was 4.8 years. Overall, 76% (28/37) returned to soccer and 5.4% (2/37) underwent revision ACLR. No major significant differences were found in demographic or surgical characteristics. No differences were found in postoperative IKDC scores, preoperative, postoperative, or change from pre-to postoperative Marx activity scores, or pre-and postoperative Tegner scores between the groups. QT autograft ACLR patients had significantly less change in Tegner scores pre-to postoperatively compared to the BTPB autograft ACLR group (0.6±1.2 versus 2.1±1.8; p=0.02). Both groups had similar rates of return to soccer [78% (18/23) BPTB autograft ACLR versus 71% (10/14) QT autograft ACLR; p=0.64] and rates of revision (8.7 % (2/23) BPTB autograft ACLR; 0 % (0/14) QT autograft ACLR.Results of this study suggest that BPTB autograft ACLR and QT autograft ACLR produce comparable, successful functional and return to soccer outcomes in this all-female soccer player cohort study. Larger, prospective studies are needed to improve the strength of conclusions and provide more information on the optimal graft choice for female soccer players. Surgeons can use the results of this study to counsel female soccer players on expected outcomes after ACLR.III.
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| 33. |
- Meredith, Sean J., et al.
(författare)
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Return to Sport After Anterior Cruciate Ligament Injury: Panther Symposium ACL Injury Return to Sport Consensus Group
- 2020
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Ingår i: Orthopaedic Journal of Sports Medicine. - : SAGE Publications. - 2325-9671. ; 8:6
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Tidskriftsartikel (refereegranskat)abstract
- Background: A precise and consistent definition of return to sport (RTS) after anterior cruciate ligament (ACL) injury is lacking, and there is controversy surrounding the process of returning patients to sport and their previous activity level. Purpose: The aim of the Panther Symposium ACL Injury Return to Sport Consensus Group was to provide a clear definition of RTS after ACL injury and a description of the RTS continuum as well as provide clinical guidance on RTS testing and decision-making. Study Design: Consensus statement. Methods: An international, multidisciplinary group of ACL experts convened as part of a consensus meeting. Consensus statements were developed using a modified Delphi method. Literature review was performed to report the supporting evidence. Results: Key points include that RTS is characterized by achievement of the preinjury level of sport and involves a criteria-based progression from return to participation to RTS and, ultimately, return to performance. Purely time-based RTS decision-making should be abandoned. Progression occurs along an RTS continuum, with decision-making by a multidisciplinary group that incorporates objective physical examination data and validated and peer-reviewed RTS tests, which should involve functional assessment as well as psychological readiness. Consideration should be given to biological healing, contextual factors, and concomitant injuries. Conclusion: The resultant consensus statements and scientific rationale aim to inform the reader of the complex process of RTS after ACL injury that occurs along a dynamic continuum. Research is needed to determine the ideal RTS test battery, the best implementation of psychological readiness testing, and methods for the biological assessment of healing and recovery.
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| 34. |
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| 35. |
- Smith, Anderson David, 1985, et al.
(författare)
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Toward CMOS compatible wafer-scale fabrication of carbon-based microsupercapacitors for IoT
- 2018
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Ingår i: Journal of Physics: Conference Series. - : IOP Publishing. - 1742-6588 .- 1742-6596. ; 1052:1
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Konferensbidrag (refereegranskat)abstract
- This work presents a wafer-scale method of microsupercapacitor (MSC) fabrication. Deposition of the electrode precursor, i.e. graphene oxide, is accomplished through spin-coating which allows for potential application in CMOS compatible processes for future integrated on-chip energy storage systems. Our MSCs have an areal capacitance of 0.4 mF/cm2at 10 μA, which is a very promising result. Further, the MSC has good rate capability as its capacitance decreases by only 0.03 mF/cm2when the current increases to 50 μA. The MSCs have a maximum energy density of 0.04 μWh/cm2and a maximum power density as high as 96 μW/cm2. Additionally, the wafer-scale process demonstrates industrial viability.
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| 36. |
- Vyas, Aditi Haresh, et al.
(författare)
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Tear film breakup time-based dry eye disease detection using convolutional neural network
- 2024
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Ingår i: Neural Computing & Applications. - : Springer. - 0941-0643 .- 1433-3058. ; 36, s. 143-161
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Tidskriftsartikel (refereegranskat)abstract
- Dry eye disease (DED) is a chronic eye disease and a common complication among the world's population. Evaporation of moisture from tear film or a decrease in tear production leads to an unstable tear film which causes DED. The tear film breakup time (TBUT) test is a common clinical test used to diagnose DED. In this test, DED is diagnosed by measuring the time at which the first breakup pattern appears on the tear film. TBUT test is subjective, labour-intensive and time-consuming. These weaknesses make a computer-aided diagnosis of DED highly desirable. The existing computer-aided DED detection techniques use expensive instruments for image acquisition which may not be available in all eye clinics. Moreover, among these techniques, TBUT-based DED detection techniques are limited to finding only tear film breakup area/time and do not identify the severity of DED, which can essentially be helpful to ophthalmologists in prescribing the right treatment. Additionally, a few challenges in developing a DED detection approach are less illuminated video, constant blinking of eyes in the videos, blurred video, and lack of public datasets. This paper presents a novel TBUT-based DED detection approach that detects the presence/absence of DED from TBUT video. In addition, the proposed approach accurately identifies the severity level of DED and further categorizes it as normal, moderate or severe based on the TBUT. The proposed approach exhibits high performance in classifying TBUT frames, detecting DED, and severity grading of TBUT video with an accuracy of 83%. Also, the correlation computed between the proposed approach and the Ophthalmologist's opinion is 90%, which reflects the noteworthy contribution of our proposed approach.
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| 37. |
- Vyas, Agin, 1992, et al.
(författare)
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Surface Roughening with Iron Nanoparticles for Promoted Adhesion of Spin Coated Microsupercapacitor Electrodes
- 2019
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Ingår i: MRS Advances. - : Springer Science and Business Media LLC. - 2059-8521. ; 4:23, s. 1335-1340
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Konferensbidrag (refereegranskat)abstract
- Microsupercapacitors (MSCs) are miniaturized energy storage devices that can be integrated in an on-chip platform as a component of a power supply for Internet of things' sensors. Integration of these on-chip MSCs require them to be fabricated through CMOS compatible fabrication techniques such as spin coating. One of the biggest challenges in spin coated MSCs is the poor surface adhesion. In this work, we present a CMOS compatible electrode deposition process with enhanced adhesion and retention for reduced graphene oxide (rGO) using spin coating. In order to improve the adhesion and surface uniformity of the deposited electrode material, the surface of Si/SiO 2 wafers was subjected to roughening through Fe nanoparticle formation. A 4 nm thick Fe layer deposition substantially magnified the average mean surface roughness of the substrates. In comparison with substrates without the Fe deposition, the treated ones have more than 300% improvement in surface coverage and rGO mass retention after sonication testing. These results suggest that the surface roughening has a positive influence on electrode deposition via a spin-coating method.
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| 39. |
- 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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