| 1. |
- Bravo, L, et al.
(författare)
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- 2021
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swepub:Mat__t
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| 2. |
- Tabiri, S, et al.
(författare)
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- 2021
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swepub:Mat__t
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| 3. |
- Lazaridis, Iosif, et al.
(författare)
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Ancient human genomes suggest three ancestral populations for present-day Europeans
- 2014
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 513:7518, s. 409-
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Tidskriftsartikel (refereegranskat)abstract
- We sequenced the genomes of a similar to 7,000-year-old farmer from Germany and eight similar to 8,000-year-old hunter-gatherers from Luxembourg and Sweden. We analysed these and other ancient genomes(1-4) with 2,345 contemporary humans to show that most present-day Europeans derive from at least three highly differentiated populations: west European hunter-gatherers, who contributed ancestry to all Europeans but not to Near Easterners; ancient north Eurasians related to Upper Palaeolithic Siberians(3), who contributed to both Europeans and Near Easterners; and early European farmers, who were mainly of Near Eastern origin but also harboured west European hunter-gatherer related ancestry. We model these populations' deep relationships and show that early European farmers had similar to 44% ancestry from a 'basal Eurasian' population that split before the diversification of other non-African lineages.
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| 4. |
- Johansson, R., et al.
(författare)
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A strategy for assessing safe use of sensors in autonomous road vehicles
- 2017
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Ingår i: 36th International Conference on Computer Safety, Reliability, and Security, SAFECOMP 2017. - Cham : Springer. - 9783319662657 ; , s. 149-161
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Konferensbidrag (refereegranskat)abstract
- When arguing safety for an autonomous road vehicle it is considered very hard to show that the sensing capability is sufficient for all possible scenarios that might occur. Already for today’s manually driven road vehicles equipped with advanced driver assistance systems (ADAS), it is far from trivial how to argue that the sensor systems are sufficiently capable of enabling a safe behavior. In this paper, we argue that the transition from ADAS to automated driving systems (ADS) enables new solution patterns for the safety argumentation dependent on the sensor systems. A key factor is that the ADS itself can compensate for a lower sensor capability, by for example lowering the speed or increasing the distances. The proposed design strategy allocates safety requirements on the sensors to determine their own capability. This capability is then to be balanced by the tactical decisions of the ADS equipped road vehicle.
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| 5. |
- DeMeo, Francesca E., et al.
(författare)
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Isolating the mechanisms for asteroid surface refreshing
- 2023
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Ingår i: Icarus. - : Elsevier. - 0019-1035 .- 1090-2643. ; 389
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Tidskriftsartikel (refereegranskat)abstract
- Evidence is seen for young, fresh surfaces among Near-Earth and Main-Belt asteroids even though space-weathering timescales are shorter than the age of the surfaces. A number of mechanisms have been proposed to refresh asteroid surfaces on short timescales, such as planetary encounters, YORP spinup, thermal degradation, and collisions. Additionally, other factors such as grain size effects have been proposed to explain the existence of these “fresh-looking” spectra. To investigate the role each of these mechanisms may play, we collected a sample of visible and near-infrared spectra of 477 near-Earth and Mars Crosser asteroids with similar sizes and compositions — all with absolute magnitude H > 16 and within the S-complex and having olivine to pyroxene (ol/(ol+opx)) ratios >0.65. We taxonomically classify these objects in the Q (fresh) and S (weathered) classes. We find four trends in the Q/S ratio: (1) previous work demonstrated the Q/S ratio increases at smaller sizes down to H ≲16, but we find a sharp increase near H∼19 after which the ratio decreases monotonically. (2) in agreement with many previous studies, the Q/S ratio increases with decreasing perihelion distance, and we find it is non-zero for larger perihelia >1.2AU, (3) as a new finding our work reveals the Q/S ratio has a sharp, significant peak near ∼5° orbital inclination, and (4) we confirm previous findings that the Q/S ratio is higher for objects that have the possibility of encounter with Earth and Venus versus those that do not, however this finding cannot be distinguished from the perihelion trend. No single resurfacing mechanism can explain all of these trends, so multiple mechanisms are required. YORP spin-up scales with size, thermal degradation is dependent on perihelion, planetary encounters trend with inclination, perihelion and MOID, noting that asteroid–asteroid collisions are also dependent on inclination. It is likely that a combination of all four resurfacing mechanisms are needed to account for all observational trends.
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| 6. |
- Eckel-Passow, Jeanette E., et al.
(författare)
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Using germline variants to estimate glioma and subtype risks
- 2019
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Ingår i: Neuro-Oncology. - : Oxford University Press. - 1522-8517 .- 1523-5866. ; 21:4, s. 451-461
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Tidskriftsartikel (refereegranskat)abstract
- Background: Twenty-five single nucleotide polymorphisms (SNPs) are associated with adult diffuse glioma risk. We hypothesized that the inclusion of these 25 SNPs with age at diagnosis and sex could estimate risk of glioma as well as identify glioma subtypes.Methods: Case-control design and multinomial logistic regression were used to develop models to estimate the risk of glioma development while accounting for histologic and molecular subtypes. Case-case design and logistic regression were used to develop models to predict isocitrate dehydrogenase (IDH) mutation status. A total of 1273 glioma cases and 443 controls from Mayo Clinic were used in the discovery set, and 852 glioma cases and 231 controls from UCSF were used in the validation set. All samples were genotyped using a custom Illumina OncoArray.Results: Patients in the highest 5% of the risk score had more than a 14-fold increase in relative risk of developing an IDH mutant glioma. Large differences in lifetime absolute risk were observed at the extremes of the risk score percentile. For both IDH mutant 1p/19q non-codeleted glioma and IDH mutant 1p/19q codeleted glioma, the lifetime risk increased from almost null to 2.3% and almost null to 1.7%, respectively. The SNP-based model that predicted IDH mutation status had a validation concordance index of 0.85.Conclusions: These results suggest that germline genotyping can provide new tools for the initial management of newly discovered brain lesions. Given the low lifetime risk of glioma, risk scores will not be useful for population screening; however, they may be useful in certain clinically defined high-risk groups.
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| 7. |
- Hanlon, Killian S., et al.
(författare)
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High levels of AAV vector integration into CRISPR-induced DNA breaks
- 2019
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Ingår i: Nature Communications. - : NATURE PUBLISHING GROUP. - 2041-1723. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- Adeno-associated virus (AAV) vectors have shown promising results in preclinical models, but the genomic consequences of transduction with AAV vectors encoding CRISPR-Cas nucleases is still being examined. In this study, we observe high levels of AAV integration (up to 47%) into Cas9-induced double-strand breaks (DSBs) in therapeutically relevant genes in cultured murine neurons, mouse brain, muscle and cochlea. Genome-wide AAV mapping in mouse brain shows no overall increase of AAV integration except at the CRISPR/Cas9 target site. To allow detailed characterization of integration events we engineer a miniature AAV encoding a 465 bp lambda bacteriophage DNA (AAV-lambda 465), enabling sequencing of the entire integrated vector genome. The integration profile of AAV-465 lambda in cultured cells display both full-length and fragmented AAV genomes at Cas9 on-target sites. Our data indicate that AAV integration should be recognized as a common outcome for applications that utilize AAV for genome editing.
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| 8. |
- Heap, Graham A., et al.
(författare)
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HLA-DQA1-HLA-DRB1 variants confer susceptibility to pancreatitis induced by thiopurine immunosuppressants
- 2014
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Ingår i: Nature Genetics. - : Nature Publishing Group. - 1061-4036 .- 1546-1718. ; 46:10, s. 1131-1134
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Tidskriftsartikel (refereegranskat)abstract
- Pancreatitis occurs in approximately 4% of patients treated with the thiopurines azathioprine or mercaptopurine. Its development is unpredictable and almost always leads to drug withdrawal. We identified patients with inflammatory bowel disease (IBD) who had developed pancreatitis within 3 months of starting these drugs from 168 sites around the world. After detailed case adjudication, we performed a genome-wide association study on 172 cases and 2,035 controls with IBD. We identified strong evidence of association within the class II HLA region, with the most significant association identified at rs2647087 (odds ratio 2.59, 95% confidence interval 2.07-3.26, P = 2 x 10(-16)). We replicated these findings in an independent set of 78 cases and 472 controls with IBD matched for drug exposure. Fine mapping of the H LA region identified association with the HLA-DQA1*02:01-HLA-DRB1*07:01 haplotype. Patients heterozygous at rs2647087 have a 9% risk of developing pancreatitis after administration of a thiopurine, whereas homozygotes have a 17% risk.
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| 9. |
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| 10. |
- Kazi, Julhash U, et al.
(författare)
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ABL2 suppresses FLT3-ITD-induced cell proliferation through negative regulation of AKT signaling
- 2017
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Ingår i: Oncotarget. - : Impact Journals, LLC. - 1949-2553. ; 8:7, s. 12194-12202
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Tidskriftsartikel (refereegranskat)abstract
- The type III receptor tyrosine kinase FLT3 is one of the most commonly mutated oncogenes in acute myeloid leukemia (AML). Inhibition of mutated FLT3 in combination with chemotherapy has displayed promising results in clinical trials. However, one of the major obstacles in targeting FLT3 is the development of resistant disease due to secondary mutations in FLT3 that lead to relapse. FLT3 and its oncogenic mutants signal through associating proteins that activate downstream signaling. Thus, targeting proteins that interact with FLT3 and their downstream signaling cascades can be an alternative approach to treat FLT3-dependent AML. We used an SH2 domain array screen to identify novel FLT3 interacting proteins and identified ABL2 as a potent interacting partner of FLT3. To understand the role of ABL2 in FLT3-mediated biological and cellular events, we used the murine pro-B cell line Ba/F3 as a model system. Overexpression of ABL2 in Ba/F3 cells expressing an oncogenic mutant of FLT3 (FLT3-ITD) resulted in partial inhibition of FLT3-ITD-dependent cell proliferation and colony formation. ABL2 expression did not alter the kinase activity of FLT3, its ubiquitination or its stability. However, it partially blocked FLT3-induced AKT phosphorylation without affecting ERK1/2 and p38 activation. Taken together our data suggest that ABL2 acts as negative regulator of signaling downstream of FLT3.
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