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- Campbell, PJ, et al.
(author)
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Pan-cancer analysis of whole genomes
- 2020
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In: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82-
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Journal article (peer-reviewed)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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- Callaway, EM, et al.
(author)
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A multimodal cell census and atlas of the mammalian primary motor cortex
- 2021
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In: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 598:7879, s. 86-102
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Journal article (peer-reviewed)abstract
- Here we report the generation of a multimodal cell census and atlas of the mammalian primary motor cortex as the initial product of the BRAIN Initiative Cell Census Network (BICCN). This was achieved by coordinated large-scale analyses of single-cell transcriptomes, chromatin accessibility, DNA methylomes, spatially resolved single-cell transcriptomes, morphological and electrophysiological properties and cellular resolution input–output mapping, integrated through cross-modal computational analysis. Our results advance the collective knowledge and understanding of brain cell-type organization1–5. First, our study reveals a unified molecular genetic landscape of cortical cell types that integrates their transcriptome, open chromatin and DNA methylation maps. Second, cross-species analysis achieves a consensus taxonomy of transcriptomic types and their hierarchical organization that is conserved from mouse to marmoset and human. Third, in situ single-cell transcriptomics provides a spatially resolved cell-type atlas of the motor cortex. Fourth, cross-modal analysis provides compelling evidence for the transcriptomic, epigenomic and gene regulatory basis of neuronal phenotypes such as their physiological and anatomical properties, demonstrating the biological validity and genomic underpinning of neuron types. We further present an extensive genetic toolset for targeting glutamatergic neuron types towards linking their molecular and developmental identity to their circuit function. Together, our results establish a unifying and mechanistic framework of neuronal cell-type organization that integrates multi-layered molecular genetic and spatial information with multi-faceted phenotypic properties.
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- Thomas, HS, et al.
(author)
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- 2019
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swepub:Mat__t
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- Chen, DS, et al.
(author)
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Single cell atlas for 11 non-model mammals, reptiles and birds
- 2021
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In: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 12:1, s. 7083-
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Journal article (peer-reviewed)abstract
- The availability of viral entry factors is a prerequisite for the cross-species transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Large-scale single-cell screening of animal cells could reveal the expression patterns of viral entry genes in different hosts. However, such exploration for SARS-CoV-2 remains limited. Here, we perform single-nucleus RNA sequencing for 11 non-model species, including pets (cat, dog, hamster, and lizard), livestock (goat and rabbit), poultry (duck and pigeon), and wildlife (pangolin, tiger, and deer), and investigated the co-expression of ACE2 and TMPRSS2. Furthermore, cross-species analysis of the lung cell atlas of the studied mammals, reptiles, and birds reveals core developmental programs, critical connectomes, and conserved regulatory circuits among these evolutionarily distant species. Overall, our work provides a compendium of gene expression profiles for non-model animals, which could be employed to identify potential SARS-CoV-2 target cells and putative zoonotic reservoirs.
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- Chen, XK, et al.
(author)
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Efficacy and Safety of Sanfu Herbal Patch at Acupoints for Persistent Allergic Rhinitis: Study Protocol for a Randomized Controlled Trial
- 2015
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In: Evidence-based complementary and alternative medicine : eCAM. - : Hindawi Limited. - 1741-427X .- 1741-4288. ; 2015, s. 214846-
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Journal article (peer-reviewed)abstract
- Background. The Sanfu herbal patch (SHP) has been widely used to treat allergic rhinitis (AR) in China. SHP has been reported to be effective for managing the symptoms of AR, but the evidence suffers from methodological limitations. Therefore, we designed a three-armed, randomized, and placebo-controlled trial to evaluate the efficacy and safety of SHP for persistent allergic rhinitis (PAR).Methods. The trial consists of 5 treatment sessions along with a one-year follow-up. This process is then repeated in the second and third years. Eligible participants diagnosed with PAR were randomized at a ratio of 2 : 2 : 1 into one of three groups: (a) SHP group; (b) placebo group; or (c) waiting-list group. The waiting-list group will receive no treatment in the first year but will receive SHP in the following two years. The primary outcome, total nasal symptoms score, is self-assessed at the beginning of each treatment session and during each annual follow-up. Secondary outcomes include the Rhinoconjunctivitis Quality-of-Life Questionnaire, allergic rhinitis attacks, and relief medications. The trial will be stopped if early termination criteria are met during the interim analysis.Ethics. This protocol has been approved by site ethics committee (number B2014-014-01) and is registered with ClinicalTrials.govNCT02192645.
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- Sun, YY, et al.
(author)
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Extramedullary Osseointegration-A Novel Design of Percutaneous Osseointegration Prosthesis for Amputees
- 2022
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In: Frontiers in bioengineering and biotechnology. - : Frontiers Media SA. - 2296-4185. ; 10, s. 811128-
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Journal article (peer-reviewed)abstract
- The percutaneous osseointegrated (OI) prostheses have greatly improved the overall quality of life for amputees. However, the long-term maintenance of the OI prostheses is still challenging. A major problem is bone resorption around the bone-implant-skin interface, which might cause implant loosening or osteomyelitis. Another problem is the breakage of connecting components between the intramedullary implant and external prosthesis due to excessive stress. We designed a novel osseointegration implant by changing the bone-implant contact from the inner cortex to the outer surface of cortical bone. In the current study, we compared the extramedullary cap-shaped implants with the intramedullary screw-type implants in rabbits. Osteointegration was confirmed at the interface of bone to implant contact (BIC) in both implant types. The external implant induced intramedullary bone regeneration in the medullary canal and increased the cortical bone density at the end of the stump. This study provides a new perspective on the design of osseointegration implants which might prevent the currently reported complications of the intramedullary OI systems.
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