| 1. |
- Niemi, MEK, et al.
(författare)
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- 2021
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swepub:Mat__t
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| 2. |
- Romagnoni, A, et al.
(författare)
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Comparative performances of machine learning methods for classifying Crohn Disease patients using genome-wide genotyping data
- 2019
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Ingår i: Scientific reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 9:1, s. 10351-
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Tidskriftsartikel (refereegranskat)abstract
- Crohn Disease (CD) is a complex genetic disorder for which more than 140 genes have been identified using genome wide association studies (GWAS). However, the genetic architecture of the trait remains largely unknown. The recent development of machine learning (ML) approaches incited us to apply them to classify healthy and diseased people according to their genomic information. The Immunochip dataset containing 18,227 CD patients and 34,050 healthy controls enrolled and genotyped by the international Inflammatory Bowel Disease genetic consortium (IIBDGC) has been re-analyzed using a set of ML methods: penalized logistic regression (LR), gradient boosted trees (GBT) and artificial neural networks (NN). The main score used to compare the methods was the Area Under the ROC Curve (AUC) statistics. The impact of quality control (QC), imputing and coding methods on LR results showed that QC methods and imputation of missing genotypes may artificially increase the scores. At the opposite, neither the patient/control ratio nor marker preselection or coding strategies significantly affected the results. LR methods, including Lasso, Ridge and ElasticNet provided similar results with a maximum AUC of 0.80. GBT methods like XGBoost, LightGBM and CatBoost, together with dense NN with one or more hidden layers, provided similar AUC values, suggesting limited epistatic effects in the genetic architecture of the trait. ML methods detected near all the genetic variants previously identified by GWAS among the best predictors plus additional predictors with lower effects. The robustness and complementarity of the different methods are also studied. Compared to LR, non-linear models such as GBT or NN may provide robust complementary approaches to identify and classify genetic markers.
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| 3. |
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| 4. |
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| 5. |
- Birney, Ewan, et al.
(författare)
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Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
- 2007
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 447:7146, s. 799-816
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Tidskriftsartikel (refereegranskat)abstract
- We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.
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| 6. |
- Craddock, Nick, et al.
(författare)
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Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls
- 2010
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 464:7289, s. 713-720
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Tidskriftsartikel (refereegranskat)abstract
- Copy number variants (CNVs) account for a major proportion of human genetic polymorphism and have been predicted to have an important role in genetic susceptibility to common disease. To address this we undertook a large, direct genome-wide study of association between CNVs and eight common human diseases. Using a purpose-designed array we typed,19,000 individuals into distinct copy-number classes at 3,432 polymorphic CNVs, including an estimated similar to 50% of all common CNVs larger than 500 base pairs. We identified several biological artefacts that lead to false-positive associations, including systematic CNV differences between DNAs derived from blood and cell lines. Association testing and follow-up replication analyses confirmed three loci where CNVs were associated with disease-IRGM for Crohn's disease, HLA for Crohn's disease, rheumatoid arthritis and type 1 diabetes, and TSPAN8 for type 2 diabetes-although in each case the locus had previously been identified in single nucleotide polymorphism (SNP)-based studies, reflecting our observation that most common CNVs that are well-typed on our array are well tagged by SNPs and so have been indirectly explored through SNP studies. We conclude that common CNVs that can be typed on existing platforms are unlikely to contribute greatly to the genetic basis of common human diseases.
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| 7. |
- Jones, Benedict C, et al.
(författare)
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To which world regions does the valence-dominance model of social perception apply?
- 2021
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Ingår i: Nature Human Behaviour. - : Springer Science and Business Media LLC. - 2397-3374. ; 5:1, s. 159-169
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Tidskriftsartikel (refereegranskat)abstract
- Over the past 10 years, Oosterhof and Todorov's valence-dominance model has emerged as the most prominent account of how people evaluate faces on social dimensions. In this model, two dimensions (valence and dominance) underpin social judgements of faces. Because this model has primarily been developed and tested in Western regions, it is unclear whether these findings apply to other regions. We addressed this question by replicating Oosterhof and Todorov's methodology across 11 world regions, 41 countries and 11,570 participants. When we used Oosterhof and Todorov's original analysis strategy, the valence-dominance model generalized across regions. When we used an alternative methodology to allow for correlated dimensions, we observed much less generalization. Collectively, these results suggest that, while the valence-dominance model generalizes very well across regions when dimensions are forced to be orthogonal, regional differences are revealed when we use different extraction methods and correlate and rotate the dimension reduction solution. PROTOCOL REGISTRATION: The stage 1 protocol for this Registered Report was accepted in principle on 5 November 2018. The protocol, as accepted by the journal, can be found at https://doi.org/10.6084/m9.figshare.7611443.v1 .
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| 8. |
- Gaulton, Kyle J, et al.
(författare)
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Genetic fine mapping and genomic annotation defines causal mechanisms at type 2 diabetes susceptibility loci.
- 2015
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 47:12, s. 1415-1415
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Tidskriftsartikel (refereegranskat)abstract
- We performed fine mapping of 39 established type 2 diabetes (T2D) loci in 27,206 cases and 57,574 controls of European ancestry. We identified 49 distinct association signals at these loci, including five mapping in or near KCNQ1. 'Credible sets' of the variants most likely to drive each distinct signal mapped predominantly to noncoding sequence, implying that association with T2D is mediated through gene regulation. Credible set variants were enriched for overlap with FOXA2 chromatin immunoprecipitation binding sites in human islet and liver cells, including at MTNR1B, where fine mapping implicated rs10830963 as driving T2D association. We confirmed that the T2D risk allele for this SNP increases FOXA2-bound enhancer activity in islet- and liver-derived cells. We observed allele-specific differences in NEUROD1 binding in islet-derived cells, consistent with evidence that the T2D risk allele increases islet MTNR1B expression. Our study demonstrates how integration of genetic and genomic information can define molecular mechanisms through which variants underlying association signals exert their effects on disease.
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| 9. |
- Regev, A, et al.
(författare)
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The Human Cell Atlas
- 2017
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Ingår i: eLife. - : ELIFE SCIENCES PUBLICATIONS LTD. - 2050-084X. ; 6
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Tidskriftsartikel (refereegranskat)
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| 10. |
- Dunham, I, et al.
(författare)
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The DNA sequence of human chromosome 22
- 1999
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 402:6761, s. 489-495
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Tidskriftsartikel (refereegranskat)
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| 11. |
- Tobin, John J., et al.
(författare)
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The VLA/ALMA Nascent Disk and Multiplicity (VANDAM) Survey of Orion Protostars. II. A Statistical Characterization of Class 0 and Class i Protostellar Disks
- 2020
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Ingår i: Astrophysical Journal. - : American Astronomical Society. - 1538-4357 .- 0004-637X. ; 890:2
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Tidskriftsartikel (refereegranskat)abstract
- We have conducted a survey of 328 protostars in the Orion molecular clouds with the Atacama Large Millimeter/submillimeter Array at 0.87 mm at a resolution of ∼0.″1 (40 au), including observations with the Very Large Array at 9 mm toward 148 protostars at a resolution of ∼0.″08 (32 au). This is the largest multiwavelength survey of protostars at this resolution by an order of magnitude. We use the dust continuum emission at 0.87 and 9 mm to measure the dust disk radii and masses toward the Class 0, Class I, and flat-spectrum protostars, characterizing the evolution of these disk properties in the protostellar phase. The mean dust disk radii for the Class 0, Class I, and flat-spectrum protostars are 44.9-3.4+5.8, 37.0-3.0+4.9, and 28.5-2.3+3.7 au, respectively, and the mean protostellar dust disk masses are 25.9-4.0+7.7, 14.9-2.2+3.8, 11.6-1.9+3.5 M⊙, respectively. The decrease in dust disk masses is expected from disk evolution and accretion, but the decrease in disk radii may point to the initial conditions of star formation not leading to the systematic growth of disk radii or that radial drift is keeping the dust disk sizes small. At least 146 protostellar disks (35% of 379 detected 0.87 mm continuum sources plus 42 nondetections) have disk radii greater than 50 au in our sample. These properties are not found to vary significantly between different regions within Orion. The protostellar dust disk mass distributions are systematically larger than those of Class II disks by a factor of >4, providing evidence that the cores of giant planets may need to at least begin their formation during the protostellar phase.
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| 12. |
- Archer, E., et al.
(författare)
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Biodiversity and ecosystem services on the African continent - What is changing, and what are our options?
- 2021
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Ingår i: Environmental Development. - : Elsevier BV. - 2211-4645 .- 2211-4653. ; 37
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Tidskriftsartikel (refereegranskat)abstract
- Throughout the world, biodiversity and nature's contributions to people are under threat, with clear changes evident. Biodiversity and ecosystem services have particular value in Africa- yet they are negatively impacted by a range of drivers, including land use and climate change. In this communication, we show evidence of changing biodiversity and ecosystem services in Africa, as well as the current most significant drivers of change. We then consider five plausible futures for the African continent, each underlain by differing assumptions. In three out of the five futures under consideration, negative impacts on biodiversity and ecosystem services are likely to persist. Those two plausible futures prioritizing environment and sustainability, however, are shown as the most likely paths to achieving long term development objectives without compromising the continent's biodiversity and ecosystem services. Such a finding shows clearly that achievement of such objectives cannot be separated from full recognition of the value of such services.
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| 13. |
- Guerriero, S., et al.
(författare)
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Systematic approach to sonographic evaluation of the pelvis in women with suspected endometriosis, including terms, definitions and measurements : A consensus opinion from the International Deep Endometriosis Analysis (IDEA) group
- 2016
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Ingår i: Ultrasound in Obstetrics & Gynecology. - : Wiley. - 0960-7692. ; 48:3, s. 318-332
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Tidskriftsartikel (refereegranskat)abstract
- The IDEA (International Deep Endometriosis Analysis group) statement is a consensus opinion on terms, definitions and measurements that may be used to describe the sonographic features of the different phenotypes of endometriosis. Currently, it is difficult to compare results between published studies because authors use different terms when describing the same structures and anatomical locations. We hope that the terms and definitions suggested herein will be adopted in centers around the world. This would result in consistent use of nomenclature when describing the ultrasound location and extent of endometriosis. We believe that the standardization of terminology will allow meaningful comparisons between future studies in women with an ultrasound diagnosis of endometriosis and should facilitate multicenter research.
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| 14. |
- Moncalvo, J. M., et al.
(författare)
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The cantharelloid clade: dealing with incongruent gene trees and phylogenetic reconstruction methods
- 2006
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Ingår i: Mycologia. - : Informa UK Limited. - 0027-5514 .- 1557-2536. ; 98:6, s. 937-948
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Tidskriftsartikel (refereegranskat)abstract
- We reassessed the circumscription of the cantharelloid clade and identified monophyletic groups by using nLSU, nSSU, mtSSU and RPB2 sequence data. Results agreed with earlier studies that placed the genera Cantharellus, Craterellus, Hydnum, Clavulina, Membranomyces, Multiclavula, Sistotrema, Botryobasidium and the family Ceratobasidiaceae in that clade. Phylogenetic analyses support monophyly of all genera except Sistotrema, which was highly polyphyletic. Strongly supported monophyletic groups were: (i) Cantharellus-Craterellus, Hydnum, and the Sistotrema confluens group; (ii) Clavulina-Membranomyces and the S. brinkmannii-oblongisporum group, with Multiclavula being possibly sister of that clade; (iii) the Sistotrema eximum-octosporum group; (iv) Sistotrema adnatum and S. coronilla. Positions of Sistotrema raduloides and S. athelioides were unresolved, as were basal relationships. Botryobasidium was well supported as the sister taxon of all the above taxa, while Ceratobasidiaceae was the most basal lineage. The relationship between Tulasnella and members of the cantharelloid clade will require further scrutiny, although there is cumulative evidence that they are probably sister groups. The rates of molecular evolution of both the large and small nuclear ribosomal RNA genes (nuc-rDNA) are much higher in Cantharellus, Craterellus and Tulasnella than in the other cantharelloid taxa, and analyses of nuc-rDNA sequences strongly placed Tulasnella close to Cantharellus-Craterellus. In contrast analyses with RPB2 and mtSSU sequences placed Tulasnella at the base of the cantharelloid clade. Our attempt to reconstruct a "supertree" from tree topologies resulting from separate analyses that avoided phylogenetic reconstruction problems associated with missing data and/or unalignable sequences proved unsuccessful.
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| 15. |
- Moshontz, Hannah, et al.
(författare)
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The Psychological Science Accelerator: Advancing Psychology Through a Distributed Collaborative Network
- 2018
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Ingår i: Advances in Methods and Practices in Psychological Science. - : SAGE Publications. - 2515-2459 .- 2515-2467. ; 1:4, s. 501-515
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Tidskriftsartikel (refereegranskat)abstract
- Concerns about the veracity of psychological research have been growing. Many findings in psychological science are based on studies with insufficient statistical power and nonrepresentative samples, or may otherwise be limited to specific, ungeneralizable settings or populations. Crowdsourced research, a type of large-scale collaboration in which one or more research projects are conducted across multiple lab sites, offers a pragmatic solution to these and other current methodological challenges. The Psychological Science Accelerator (PSA) is a distributed network of laboratories designed to enable and support crowdsourced research projects. These projects can focus on novel research questions or replicate prior research in large, diverse samples. The PSA’s mission is to accelerate the accumulation of reliable and generalizable evidence in psychological science. Here, we describe the background, structure, principles, procedures, benefits, and challenges of the PSA. In contrast to other crowdsourced research networks, the PSA is ongoing (as opposed to time limited), efficient (in that structures and principles are reused for different projects), decentralized, diverse (in both subjects and researchers), and inclusive (of proposals, contributions, and other relevant input from anyone inside or outside the network). The PSA and other approaches to crowdsourced psychological science will advance understanding of mental processes and behaviors by enabling rigorous research and systematic examination of its generalizability.
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| 16. |
- Tobin, J. J., et al.
(författare)
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A triple protostar system formed via fragmentation of a gravitationally unstable disk
- 2016
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 538:7626, s. 483-
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Tidskriftsartikel (refereegranskat)abstract
- Binary and multiple star systems are a frequent outcome of the star formation process(1,2) and as a result almost half of all stars with masses similar to that of the Sun have at least one companion star(3). Theoretical studies indicate that there are two main pathways that can operate concurrently to form binary/multiple star systems: large-scale fragmentation of turbulent gas cores and filaments(4,5) or smaller-scale fragmentation of a massive protostellar disk due to gravitational instability(6,7). Observational evidence for turbulent fragmentation on scales of more than 1,000 astronomical units has recently emerged(8,9). Previous evidence for disk fragmentation was limited to inferences based on the separations of more-evolved pre-main sequence and protostellar multiple systems(10-13). The triple protostar system L1448 IRS3B is an ideal system with which to search for evidence of disk fragmentation as it is in an early phase of the star formation process, it is likely to be less than 150,000 years old(14) and all of the protostars in the system are separated by less than 200 astronomical units. Here we report observations of dust and molecular gas emission that reveal a disk with a spiral structure surrounding the three protostars. Two protostars near the centre of the disk are separated by 61 astronomical units and a tertiary protostar is coincident with a spiral arm in the outer disk at a separation of 183 astronomical units(13). The inferred mass of the central pair of protostellar objects is approximately one solar mass, while the disk surrounding the three protostars has a total mass of around 0.30 solar masses. The tertiary protostar itself has a minimum mass of about 0.085 solar masses. We demonstrate that the disk around L1448 IRS3B appears susceptible to disk fragmentation at radii between 150 and 320 astronomical units, overlapping with the location of the tertiary protostar. This is consistent with models for a protostellar disk that has recently undergone gravitational instability, spawning one or two companion stars.
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| 17. |
- Tobin, John J., et al.
(författare)
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The VLA/ALMA Nascent Disk and Multiplicity (VANDAM) Survey of Orion Protostars. I. Identifying and Characterizing the Protostellar Content of the OMC-2 FIR4 and OMC-2 FIR3 Regions
- 2019
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Ingår i: Astrophysical Journal. - : American Astronomical Society. - 1538-4357 .- 0004-637X. ; 886:1
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Tidskriftsartikel (refereegranskat)abstract
- We present Atacama Large Millimeter/submillimeter Array (0.87 mm) and Very Large Array (9 mm) observations toward OMC-2 FIR4 and OMC-2 FIR3 within the Orion integral-shaped filament, thought to be two of the nearest regions of intermediate-mass star formation. We characterize the continuum sources within these regions on ?40 au (01) scales and associated molecular line emission at a factor of ?30 better resolution than previous observations at similar wavelengths. We identify six compact continuum sources within OMC-2 FIR4, four in OMC-2 FIR3, and one additional source just outside OMC-2 FIR4. This continuum emission is tracing the inner envelope and/or disk emission on less than 100 au scales. HOPS-108 is the only protostar in OMC-2 FIR4 that exhibits emission from high-excitation transitions of complex organic molecules (e.g., methanol and other lines) coincident with the continuum emission. HOPS-370 in OMC-2 FIR3, with L;?;360 L, also exhibits emission from high-excitation methanol and other lines. The methanol emission toward these two protostars is indicative of temperatures high enough to thermally evaporate it from icy dust grains; overall, these protostars have characteristics similar to hot corinos. We do not identify a clear outflow from HOPS-108 in (CO)-C-12, but we find evidence of interaction between the outflow/jet from HOPS-370 and the OMC-2 FIR4 region. A multitude of observational constraints indicate that HOPS-108 is likely a low- to intermediate-mass protostar in its main mass accretion phase and is the most luminous protostar in OMC-2 FIR4. The high-resolution data presented here are essential for disentangling the embedded protostars from their surrounding dusty environments and characterizing them.
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| 18. |
- Svoboda, B. E., et al.
(författare)
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THE BOLOCAM GALACTIC PLANE SURVEY. XIV. PHYSICAL PROPERTIES of MASSIVE STARLESS and STAR-FORMING CLUMPS
- 2016
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Ingår i: Astrophysical Journal. - 0004-637X .- 1538-4357. ; 822:2
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Tidskriftsartikel (refereegranskat)abstract
- We sort 4683 molecular clouds between 10° < ℓ < 65° from the Bolocam Galactic Plane Survey based on observational diagnostics of star formation activity: compact 70 μm sources, mid-IR color-selected YSOs, H2O and CH3OH masers, and UCH ii regions. We also present a combined NH3-derived gas kinetic temperature and H2O maser catalog for 1788 clumps from our own GBT 100 m observations and from the literature. We identify a subsample of 2223 (47.5%) starless clump candidates (SCCs), the largest and most robust sample identified from a blind survey to date. Distributions of flux density, flux concentration, solid angle, kinetic temperature, column density, radius, and mass show strong (>1 dex) progressions when sorted by star formation indicator. The median SCC is marginally subvirial (α ∼ 0.7) with >75% of clumps with known distance being gravitationally bound (α < 2). These samples show a statistically significant increase in the median clump mass of ΔM ∼ 170-370 M o from the starless candidates to clumps associated with protostars. This trend could be due to (i) mass growth of the clumps at M o Myr-1 for an average freefall 0.8 Myr timescale, (ii) a systematic factor of two increase in dust opacity from starless to protostellar phases, and/or (iii) a variation in the ratio of starless to protostellar clump lifetime that scales as ∼M -0.4. By comparing to the observed number of CH3OH maser containing clumps, we estimate the phase lifetime of massive (M > 103 M o) starless clumps to be 0.37 ± 0.08 Myr (M/103 M o)-1; the majority (M < 450 M o) have phase lifetimes longer than their average freefall time. © 2016. The American Astronomical Society. All rights reserved.
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| 19. |
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| 20. |
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| 21. |
- Rada-Iglesias, Alvaro, et al.
(författare)
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Butyrate mediates decrease of histone acetylation centered on transcription start sites and down-regulation of associated genes
- 2007
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Ingår i: Genome Research. - : Cold Spring Harbor Laboratory. - 1088-9051 .- 1549-5469. ; 17:6, s. 708-719
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Tidskriftsartikel (refereegranskat)abstract
- Butyrate is a histone deacetylase inhibitor (HDACi) with anti-neoplastic properties, which theoretically reactivates epigenetically silenced genes by increasing global histone acetylation. However, recent studies indicate that a similar number or even more genes are down-regulated than up-regulated by this drug. We treated hepatocarcinoma HepG2 cells with butyrate and characterized the levels of acetylation at DNA-bound histones H3 and H4 by ChIP-chip along the ENCODE regions. In contrast to the global increases of histone acetylation, many genomic regions close to transcription start sites were deacetylated after butyrate exposure. In order to validate these findings, we found that both butyrate and trichostatin A treatment resulted in histone deacetylation at selected regions, while nucleosome loss or changes in histone H3 lysine 4 trimethylation (H3K4me3) did not occur in such locations. Furthermore, similar histone deacetylation events were observed when colon adenocarcinoma HT-29 cells were treated with butyrate. In addition, genes with deacetylated promoters were down-regulated by butyrate, and this was mediated at the transcriptional level by affecting RNA polymerase II (POLR2A) initiation/elongation. Finally, the global increase in acetylated histones was preferentially localized to the nuclear periphery, indicating that it might not be associated to euchromatin. Our results are significant for the evaluation of HDACi as anti-tumourogenic drugs, suggesting that previous models of action might need to be revised, and provides an explanation for the frequently observed repression of many genes during HDACi treatment.
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| 22. |
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| 23. |
- Almquist, Martin, et al.
(författare)
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Elastic wave propagation in anisotropic solids using energy-stable finite differences with weakly enforced boundary and interface conditions
- 2021
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Ingår i: Journal of Computational Physics. - : Elsevier. - 0021-9991 .- 1090-2716. ; 424
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Tidskriftsartikel (refereegranskat)abstract
- Summation-by-parts (SBP) finite difference methods have several desirable properties for second-order wave equations. They combine the computational efficiency of narrow-stencil finite difference operators with provable stability on curvilinear multiblock grids. While several techniques for boundary and interface conditions exist, weak imposition via simultaneous approximation terms (SATs) is perhaps the most flexible one. Although SBP methods have been applied to elastic wave equations many times, an SBP-SAT method for general anisotropic elastic wave equations has not yet been presented in the literature. We fill this gap by deriving energy-stable self-adjoint SBP-SAT methods for general anisotropic materials on curvilinear multiblock grids. The methods are based on fully compatible SBP operators. Although this paper focuses on classical SBP finite difference operators, the presented boundary and interface treatments are general and apply to a range of methods that satisfy an SBP property. We demonstrate the stability and accuracy properties of a particular set of fully compatible SBP-SAT schemes using the method of manufactured solutions. We also demonstrate the utility of the new method in elastodynamic cloaking and seismic imaging in mountainous regions.
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| 24. |
- Almquist, Martin, et al.
(författare)
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Non-stiff boundary and interface penalties for narrow-stencil finite difference approximations of the Laplacian on curvilinear multiblock grids
- 2020
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Ingår i: Journal of Computational Physics. - : Elsevier BV. - 0021-9991 .- 1090-2716. ; 408
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Tidskriftsartikel (refereegranskat)abstract
- The Laplacian appears in several partial differential equations used to model wave propagation. Summation-by-parts simultaneous approximation term (SBP-SAT) finite difference methods are often used for such equations, as they combine computational efficiency with provable stability on curvilinear multiblock grids. However, the existing SBP-SAT discretization of the Laplacian quickly becomes prohibitively stiff as grid skewness increases. The stiffness stems from the SATs that impose inter-block couplings and Dirichlet boundary conditions. We resolve this issue by deriving stable SATs whose stiffness is almost insensitive to grid skewness. The new discretization thus allows for large time steps in explicit time integrators, even on very skewed grids. It also applies to the variable-coefficient generalization of the Laplacian. We demonstrate the efficacy and versatility of the new SATs by applying them to acoustic wave propagation problems inspired by marine seismic exploration and infrasound monitoring of volcanoes.
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| 25. |
- Bader, Milad, et al.
(författare)
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Modeling and inversion in acoustic-elastic coupled media using energy-stable summation-by-parts operators
- 2023
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Ingår i: Geophysics. - : SOC EXPLORATION GEOPHYSICISTS - SEG. - 0016-8033 .- 1942-2156. ; 88:3
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Tidskriftsartikel (refereegranskat)abstract
- Seismic data acquired at the seafloor are valuable in charac-terizing the subsurface and monitoring producing hydrocarbon fields. To fully use such data, a stable, accurate, and efficient numerical scheme is needed that accounts for acoustic and elas-tic wave propagation, their interaction at the seafloor interface, and for sources and receivers placed on either side of that inter-face. Existing methods either make incorrect assumptions or have high implementation and computational costs. We have developed a high-order finite-difference summation-by-parts framework for the acoustic-elastic wave equations in second -or-der form (in terms of displacements in the solid and an extension of velocity potential in the fluid). Our modified discretization of the elastic operator overcomes the dispersion errors known to plague displacement-based schemes in the high VP/VS limit. We weakly impose boundary and interface conditions using simulta-neous approximation terms, leading to an energy-stable numeri-cal scheme that rigorously handles point injection and extraction. The fully discrete system is self-adjoint after a time reversal and a sign flip and is furthermore a high-order accurate discretization of the continuous problem. The self-adjointness ensures that for-ward and adjoint wavefields are computed with similar accuracy and simplifies gradient computation for inversion purposes. We find that our numerical scheme achieves accuracy comparable to a more computationally expensive spectral-element method and demonstrate its application to full-waveform inversion using the Marmousi2 model.
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| 26. |
- Buckley, Patrick G, et al.
(författare)
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A full-coverage, high-resolution human chromosome 22 genomic microarrayfor clinical and research applications
- 2002
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Ingår i: Human Molecular Genetics. - : Oxford University Press (OUP). - 0964-6906 .- 1460-2083. ; 11:25, s. 3221-3229
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Tidskriftsartikel (refereegranskat)abstract
- We have constructed the first comprehensive microarray representing a human chromosome for analysis of DNA copy number variation. This chromosome 22 array covers 34.7 Mb, representing 1.1% of the genome, with an average resolution of 75 kb. To demonstrate the utility of the array, we have applied it to profile acral melanoma, dermatofibrosarcoma, DiGeorge syndrome and neurofibromatosis 2. We accurately diagnosed homozygous/heterozygous deletions, amplifications/gains, IGLV/IGLC locus instability, and breakpoints of an imbalanced translocation. We further identified the 14-3-3 eta isoform as a candidate tumor suppressor in glioblastoma. Two significant methodological advances in array construction were also developed and validated. These include a strictly sequence defined, repeat-free, and non-redundant strategy for array preparation. This approach allows an increase in array resolution and analysis of any locus; disregarding common repeats, genomic clone availability and sequence redundancy. In addition, we report that the application of phi29 DNA polymerase is advantageous in microarray preparation. A broad spectrum of issues in medical research and diagnostics can be approached using the array. This well annotated and gene-rich autosome contains numerous uncharacterized disease genes. It is therefore crucial to associate these genes to specific 22q-related conditions and this array will be instrumental towards this goal. Furthermore, comprehensive epigenetic profiling of 22q-located genes and high-resolution analysis of replication timing across the entire chromosome can be studied using our array.
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| 27. |
- Coppess, Katherine R., et al.
(författare)
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Ultra and Very Long Period Seismic Signatures of Unsteady Eruptions Predicted From Conduit Flow Models
- 2022
-
Ingår i: Journal of Geophysical Research - Solid Earth. - : American Geophysical Union (AGU). - 2169-9313 .- 2169-9356. ; 127:6
-
Tidskriftsartikel (refereegranskat)abstract
- Explosive volcanic eruptions radiate seismic waves as a consequence of pressure and shear traction changes within the conduit/chamber system. Kinematic source inversions utilize these waves to determine equivalent seismic force and moment tensor sources, but relation to eruptive processes is often ambiguous and nonunique. In this work, we provide an alternative, forward modeling approach to calculate moment tensor and force equivalents of a model of eruptive conduit flow and chamber depressurization. We explain the equivalence of two seismic force descriptions, the first in terms of traction changes on conduit/chamber walls, and the second in terms of changes in magma momentum, weight, and momentum transfer to the atmosphere. Eruption onset is marked by a downward seismic force, associated with loss of restraining shear tractions from fragmentation. This is followed by a much larger upward seismic force from upward drag of ascending magma and reduction of magma weight remaining in the conduit/chamber system. The static force is upward, arising from weight reduction. We calculate synthetic seismograms to examine the expression of eruptive processes at different receiver distances. Filtering these synthetics to the frequency band typically resolved by broadband seismometers produces waveforms similar to very long period seismic events observed in strombolian and vulcanian eruptions. However, filtering heavily distorts waveforms, accentuating processes in early, unsteady parts of eruptions and eliminating information about longer (ultra long period time scale depressurization and weight changes that dominate unfiltered seismograms. Our workflow can be utilized to directly and quantitatively connect eruption models with seismic observations.Plain Language SummaryVolcanic eruptions radiate seismic waves that can be recorded by seismometers placed on and around a volcano. Analysis of seismic data enables one to study eruptions, in particular the processes occurring in the magma-filled conduit and chamber that feeds the eruption. One process of particular interest is fragmentation, in which magma containing a mixture of liquid melt and gas bubbles breaks apart in the conduit and erupts explosively from the vent. We perform computer simulations of explosive eruptions and then use the output of those simulations to predict seismic radiation. We examine the seismograms produced by this workflow to identify features that are diagnostic of process, such as fragmentation, that occur at different times in the eruption. These predictions will guide interpretation of seismic data from real eruptions.
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| 28. |
- Dunham, Christine M., et al.
(författare)
-
Structures of tRNAs with an expanded anticodon loop in the decoding center of the 30S ribosomal subunit
- 2007
-
Ingår i: RNA. - : Cold Spring Harbor Laboratory. - 1355-8382 .- 1469-9001. ; 13:6, s. 817-823
-
Tidskriftsartikel (refereegranskat)abstract
- During translation, some +1 frameshift mRNA sites are decoded by frameshift suppressor tRNAs that contain an extra base in their anticodon loops. Similarly engineered tRNAs have been used to insert nonnatural amino acids into proteins. Here, we report crystal structures of two anticodon stem–loops (ASLs) from tRNAs known to facilitate +1 frameshifting bound to the 30S ribosomal subunit with their cognate mRNAs. ASLCCCG and ASLACCC (5'–3' nomenclature) form unpredicted anticodon–codon interactions where the anticodon base 34 at the wobble position contacts either the fourth codon base or the third and fourth codon bases. In addition, we report the structure of ASLACGA bound to the 30S ribosomal subunit with its cognate mRNA. The tRNA containing this ASL was previously shown to be unable to facilitate +1 frameshifting in competition with normal tRNAs (Hohsaka et al. 2001), and interestingly, it displays a normal anticodon–codon interaction. These structures show that the expanded anticodon loop of +1 frameshift promoting tRNAs are flexible enough to adopt conformations that allow three bases of the anticodon to span four bases of the mRNA. Therefore it appears that normal triplet pairing is not an absolute constraint of the decoding center.
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| 29. |
- Dunham, S. M., et al.
(författare)
-
Species richness and community composition of mat-forming ectomycorrhizal fungi in old- and second-growth Douglas-fir forests of the HJ Andrews Experimental Forest, Oregon, USA
- 2007
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Ingår i: Mycorrhiza. - : Springer Science and Business Media LLC. - 0940-6360 .- 1432-1890. ; 17:8, s. 633-645
-
Tidskriftsartikel (refereegranskat)abstract
- We investigated the species identity of mat-forming ectomycorrhizal (EM) fungi associated with old- and second-growth Douglas-fir stands. Using molecular analyses of rhizomorphs and EM root tips, we characterized 28 unique internal transcribed spacer sequences and considered them proxies for mat-forming EM species. In both stand age classes, one Athelioid species in the genus Piloderma dominated our sample of the mat-forming fungal community. In second-growth stands, the second most frequently encountered mat-forming EM species belonged to the genus Hysterangium. In old-growth stands, several Ramaria species were associated with a frequently encountered mat morphology but no species dominated the community. After using rarefaction analysis to standardize sampling effort, the total species richness did not differ statistically between old- and second-growth habitats. Both an abundance of infrequently encountered species and incomplete sampling of the mat-forming EM community may have limited our ability to detect potential differences in species richness. Several frequently encountered Piloderma species appear to have broad (holarctic) distributions and diverse host associations and their potential importance in forest ecosystems warrants further study.
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| 30. |
- Erickson, Brittany A., et al.
(författare)
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Incorporating Full Elastodynamic Effects and Dipping Fault Geometries in Community Code Verification Exercises for Simulations of Earthquake Sequences and Aseismic Slip (SEAS)
- 2023
-
Ingår i: Bulletin of The Seismological Society of America (BSSA). - : SEISMOLOGICAL SOC AMER. - 0037-1106 .- 1943-3573. ; 113:2, s. 499-523
-
Tidskriftsartikel (refereegranskat)abstract
- Numerical modeling of earthquake dynamics and derived insight for seismic hazard relies on credible, reproducible model results. The sequences of earthquakes and aseismic slip (SEAS) initiative has set out to facilitate community code comparisons, and verify and advance the next generation of physics-based earthquake models that reproduce all phases of the seis-mic cycle. With the goal of advancing SEAS models to robustly incorporate physical and geo-metrical complexities, here we present code comparison results from two new benchmark problems: BP1-FD considers full elastodynamic effects, and BP3-QD considers dipping fault geometries. Seven and eight modeling groups participated in BP1-FD and BP3-QD, respectively, allowing us to explore these physical ingredients across multiple codes and better understand associated numerical considerations. With new comparison metrics, we find that numerical resolution and computational domain size are critical parameters to obtain matching results. Codes for BP1-FD implement different criteria for switching between quasi-static and dynamic solvers, which require tuning to obtain matching results. In BP3-QD, proper remote boundary conditions consistent with specified rigid body translation are required to obtain matching surface displacements. With these numerical and mathematical issues resolved, we obtain excellent quantitative agreements among codes in earthquake interevent times, event moments, and coseismic slip, with reasonable agreements made in peak slip rates and rupture arrival time. We find that including full inertial effects generates events with larger slip rates and rupture speeds compared to the quasi-dynamic counterpart. For BP3-QD, both dip angle and sense of motion (thrust versus normal faulting) alter ground motion on the hanging and foot walls, and influence event patterns, with some sequences exhibiting similar-size character-istic earthquakes, and others exhibiting different-size events. These findings underscore the importance of considering full elastodynamics and nonvertical dip angles in SEAS models, as both influence short-and long-term earthquake behavior and are relevant to seismic hazard.
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| 31. |
- Heimisson, Elias R., et al.
(författare)
-
Poroelastic effects destabilize mildly rate-strengthening friction to generate stable slow slip pulses
- 2019
-
Ingår i: Journal of the mechanics and physics of solids. - : Elsevier BV. - 0022-5096 .- 1873-4782. ; 130, s. 262-279
-
Tidskriftsartikel (refereegranskat)abstract
- Slow slip events on tectonic faults, sliding instabilities that never accelerate to inertially limited ruptures or earthquakes, are one of the most enigmatic phenomena in frictional sliding. While observations of slow slip events continue to mount, a plausible mechanism that permits instability while simultaneously limiting slip speed remains elusive. Rate-and-state friction has been successful in describing most aspects of rock friction, faulting, and earthquakes; current explanations of slow slip events appeal to rate-weakening friction to induce instabilities, which are then stalled by additional stabilizing processes like dilatancy or a transition to rate-strengthening friction at high slip rates. However, the temperatures and/or clay-rich compositions at slow slip locations are almost ubiquitously associated with rate-strengthening friction. In this study, we propose a fundamentally different instability mechanism that may reconcile this contradiction, demonstrating how slow slip events can nucleate with mildly rate-strengthening friction. We identify two destabilizing mechanisms, both reducing frictional shear strength through reductions in effective normal stress, that counteract the stabilizing effects of rate-strengthening friction. The instability develops into slow slip pulses. We quantify parameter controls on pulse length, propagation speed, and other characteristics, and demonstrate broad consistency with observations of tectonic slow slip events as well as laboratory tribology experiments.
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| 32. |
- Jallow, Muminatou, et al.
(författare)
-
Genome-wide and fine-resolution association analysis of malaria in West Africa.
- 2009
-
Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; , s. 657-665
-
Tidskriftsartikel (refereegranskat)abstract
- We report a genome-wide association (GWA) study of severe malaria in The Gambia. The initial GWA scan included 2,500 children genotyped on the Affymetrix 500K GeneChip, and a replication study included 3,400 children. We used this to examine the performance of GWA methods in Africa. We found considerable population stratification, and also that signals of association at known malaria resistance loci were greatly attenuated owing to weak linkage disequilibrium (LD). To investigate possible solutions to the problem of low LD, we focused on the HbS locus, sequencing this region of the genome in 62 Gambian individuals and then using these data to conduct multipoint imputation in the GWA samples. This increased the signal of association, from P = 4 x 10(-7) to P = 4 x 10(-14), with the peak of the signal located precisely at the HbS causal variant. Our findings provide proof of principle that fine-resolution multipoint imputation, based on population-specific sequencing data, can substantially boost authentic GWA signals and enable fine mapping of causal variants in African populations.
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| 33. |
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| 34. |
- Kozdon, Jeremy E., et al.
(författare)
-
Interaction of waves with frictional interfaces using summation-by-parts difference operators : Weak enforcement of nonlinear boundary conditions
- 2011
-
Rapport (refereegranskat)abstract
- We present a high-order difference method for problems in elastodynamics involving the interaction of waves with highly nonlinear frictional interfaces. We restrict our attention to two-dimensional antiplane problems involving deformation in only one direction. Jump conditions that relate tractions on the interface, or fault, to the relative sliding velocity across it are of a form closely related to those used in earthquake rupture models and other frictional sliding problems. By using summation-by-parts (SBP) finite difference operators and weak enforcement of boundary and interface conditions, a strictly stable method is developed. Furthermore, it is shown that unless the nonlinear interface conditions are formulated in terms of characteristic variables, as opposed to the physical variables in terms of which they are more naturally stated, the semi-discretized system of equations can become extremely stiff, preventing efficient solution using explicit time integrators. The use of SBP operators also provides a rigorously defined energy balance for the discretized problem that, as the mesh is refined, approaches the exact energy balance in the continuous problem. This enables one to investigate earthquake energetics, for example the efficiency with which elastic strain energy released during rupture is converted to radiated energy carried by seismic waves, rather than dissipated by frictional sliding of the fault. These theoretical results are confirmed by several numerical tests in both one and two dimensions demonstrating the computational efficiency, the high-order convergence rate of the method, the benefits of using strictly stable numerical methods for long time integration, and the accuracy of the energy balance.
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| 35. |
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| 36. |
- Kozdon, Jeremy E., et al.
(författare)
-
Interaction of waves with frictional interfaces using summation-by-parts difference operators I : Weak enforcement of nonlinear boundary conditions
- 2010
-
Rapport (övrigt vetenskapligt/konstnärligt)abstract
- In this work we develop a high-order method for problems in scalar elastodynamics with nonlinear boundary conditions in a form closely related to those seen in earthquake rupture modeling and other frictional sliding problems. By using summation-by-parts finite difference operators and weak enforcement of boundary conditions with the simultaneous approximation term method, a strictly stable method is developed that dissipates energy at a slightly faster rate than the continuous solution (with the difference in energy dissipation rates vanishing as the mesh is refined). Furthermore, it is shown that unless boundary conditions are formulated in terms of characteristic variables, as opposed to the physical variables in terms of which boundary conditions are more naturally stated, the semi-discretized system of equations can become extremely stiff, preventing efficient solution using explicit time integrators.These theoretical results are confirmed by several numerical tests demonstrating the high-order convergence rate of the method and the benefits of using strictly stable numerical methods for long time integration.
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| 37. |
- Kozdon, Jeremy E., et al.
(författare)
-
Interaction of waves with frictional interfaces using summation-by-parts difference operators II : Extension to full elastodynamics
- 2010
-
Rapport (övrigt vetenskapligt/konstnärligt)abstract
- Problems in elastodynamics with nonlinear boundary conditions, such as those arising when modeling earthquake rupture propagation along internal interfaces (faults) governed by nonlinear friction laws, are inherently boundary driven. For such problems, stable and accurate enforcement of boundary conditions is essential for obtaining globally accurate numerical solutions (and predictions of ground motion in earthquake simulations). High-order finite difference methods are a natural choice for problems like these involving wave propagation, but enforcement of boundary conditions is complicated by the fact that the stencil must transition to one-sided near the boundary.In this work we develop a high-order method for tensor elasticity with faults whose strength is a nonlinear function of sliding velocity and a set of internal state variables obeying differential evolution equations (a mathematical framework known as rate-and-state friction). The method is based on summation-by-parts finite difference operators and weak enforcement of boundary conditions using the simultaneous approximation term method. We prove that the method is strictly stable and dissipates energy at a slightly faster rate than the continuous solution (with the difference in energy dissipation rates vanishing as the mesh is refined)
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| 38. |
- Kozdon, Jeremy E., et al.
(författare)
-
Interaction of Waves with Frictional Interfaces Using Summation-by-Parts Difference Operators: Weak Enforcement of Nonlinear Boundary Conditions
- 2012
-
Ingår i: Journal of Scientific Computing. - : Springer. - 0885-7474 .- 1573-7691. ; 50:2, s. 341-367
-
Tidskriftsartikel (refereegranskat)abstract
- We present a high-order difference method for problems in elastodynamics involving the interaction of waves with highly nonlinear frictional interfaces. We restrict our attention to two-dimensional antiplane problems involving deformation in only one direction. Jump conditions that relate tractions on the interface, or fault, to the relative sliding velocity across it are of a form closely related to those used in earthquake rupture models and other frictional sliding problems. By using summation-by-parts (SBP) finite difference operators and weak enforcement of boundary and interface conditions, a strictly stable method is developed. Furthermore, it is shown that unless the nonlinear interface conditions are formulated in terms of characteristic variables, as opposed to the physical variables in terms of which they are more naturally stated, the semi-discretized system of equations can become extremely stiff, preventing efficient solution using explicit time integrators. The use of SBP operators also provides a rigorously defined energy balance for the discretized problem that, as the mesh is refined, approaches the exact energy balance in the continuous problem. This enables one to investigate earthquake energetics, for example the efficiency with which elastic strain energy released during rupture is converted to radiated energy carried by seismic waves, rather than dissipated by frictional sliding of the fault. These theoretical results are confirmed by several numerical tests in both one and two dimensions demonstrating the computational efficiency, the high-order convergence rate of the method, the benefits of using strictly stable numerical methods for long time integration, and the accuracy of the energy balance.
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| 39. |
- Kozdon, Jeremy E., et al.
(författare)
-
Simulation of Dynamic Earthquake Ruptures in Complex Geometries Using High-Order Finite Difference Methods
- 2012
-
Rapport (övrigt vetenskapligt/konstnärligt)abstract
- We develop a stable and high-order accurate finite difference method for problems in earthquake rupture dynamics capable of handling complex geometries and multiple faults. The bulk material is an isotropic elastic solid cut by preexisting fault interfaces. The fields across the interfaces are related through friction laws which depend on the sliding velocity, tractions acting on the interface, and state variables which evolve according to ordinary differential equations involving local fields. The method is based on summation-by-parts finite difference operators with irregular geometries handled through coordinate transforms and multi-block meshes. Boundary conditions as well as block interface conditions (whether frictional or otherwise) are enforced weakly through the simultaneous approximation term method, resulting in a provably stable discretization. The theoretical accuracy and stability results are confirmed with the method of manufactured solutions. The practical benefits of the new methodology are illustrated in a simulation of a subduction zone megathrust earthquake, a challenging application problem involving complex free-surface topography, nonplanar faults, and varying material properties.
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| 40. |
- Kozdon, Jeremy E., et al.
(författare)
-
Simulation of Dynamic Earthquake Ruptures in Complex Geometries Using High-Order Finite Difference Methods
- 2013
-
Ingår i: Journal of Scientific Computing. - : Springer. - 0885-7474 .- 1573-7691. ; 55:1, s. 92-124
-
Tidskriftsartikel (refereegranskat)abstract
- We develop a stable and high-order accurate finite difference method for problems in earthquake rupture dynamics in complex geometries with multiple faults. The bulk material is an isotropic elastic solid cut by pre-existing fault interfaces that accommodate relative motion of the material on the two sides. The fields across the interfaces are related through friction laws which depend on the sliding velocity, tractions acting on the interface, and state variables which evolve according to ordinary differential equations involving local fields. The method is based on summation-by-parts finite difference operators with irregular geometries handled through coordinate transforms and multi-block meshes. Boundary conditions as well as block interface conditions (whether frictional or otherwise) are enforced weakly through the simultaneous approximation term method, resulting in a provably stable discretization. The theoretical accuracy and stability results are confirmed with the method of manufactured solutions. The practical benefits of the new methodology are illustrated in a simulation of a subduction zone megathrust earthquake, a challenging application problem involving complex free-surface topography, nonplanar faults, and varying material properties.
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| 41. |
- Lutzhoft, Margareta, et al.
(författare)
-
Maritime research
- 2017
-
Ingår i: Simulators for Transportation Human Factors. - Boca Raton : Taylor & Francis, CRC Press, 2017. | Series: The Human factors of simulation and assessment : Taylor & Francis Group. - 9781472411433
-
Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- Simulation continues to be a growth area in transportation human factors. From empirical studies in the laboratory to the latest training techniques in the field, simulators offer myriad benefits for the experimenter and the practitioner. This book draws together current trends in research and training simulators for the road, rail, air and sea sectors to inform the reader how to maximize both validity and cost-effectiveness in each case. Simulators for Transportation Human Factors provides a valuable resource for both researchers and practitioners in transportation human factors on the use of simulators, giving readers concrete examples and case studies of how simulators have been developed and used in empirical research as well as training applications. It offers useful and usable information on the functional requirements of simulators without the need for any background knowledge on the technical aspects, focusing on the state of the art of research and applications in transport simulators rather than the state of the art of simulation technology. The book covers simulators in operational terms instead of task simulation/modelling and provides a useful balance between a bottom-up, academic approach and a top-down, practical perspective.
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| 42. |
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| 43. |
- Meisner, Jeffrey, et al.
(författare)
-
Structure of the basal components of a bacterial transporter
- 2012
-
Ingår i: Proceedings of the National Academy of Sciences. - : Proceedings of the National Academy of Sciences. - 1091-6490 .- 0027-8424. ; 109:14, s. 5446-5451
-
Tidskriftsartikel (refereegranskat)abstract
- Proteins SpoIIQ and SpoIIIAH interact through two membranes to connect the forespore and the mother cell during endospore development in the bacterium Bacillus subtilis. SpoIIIAH consists of a transmembrane segment and an extracellular domain with similarity to YscJ proteins. YscJ proteins form large multimeric rings that are the structural scaffolds for the assembly of type III secretion systems in Gram-negative bacteria. The predicted ring-forming motif of SpoIIIAH and other evidence led to the model that SpoIIQ and SpoIIIAH form the core components of a channel or transporter through which the mother cell nurtures forespore development. Therefore, to understand the roles of SpoIIIAH and SpoIIQ in channel formation, it is critical to determine whether SpoIIIAH adopts a ring-forming structural motif, and whether interaction of SpoIIIAH with SpoIIQ would preclude ring formation. We report a 2.8-angstrom resolution structure of a complex of SpoIIQ and SpoIIIAH. SpoIIIAH folds into the ring-building structural motif, and modeling shows that the structure of the SpoIIQ-SpoIIIAH complex is compatible with forming a symmetrical oligomer that is similar to those in type III systems. The inner diameters of the two most likely ring models are large enough to accommodate several copies of other integral membrane proteins. SpoIIQ contains a LytM domain, which is found in metalloendopeptidases, but lacks residues important for metalloprotease activity. Other LytM domains appear to be involved in protein-protein interactions. We found that the LytM domain of SpoIIQ contains an accessory region that interacts with SpoIIIAH.
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| 44. |
- O´Reilly, Ossian, et al.
(författare)
-
Coupled High-Order Finite Difference and Unstructured Finite Volume Methods for Earthquake Rupture Dynamics in Complex Geometries
- 2011
-
Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Unstructured grid methods are well suited for earthquake problems in complex geometries, such as non-planar and branching faults. Unfortunately they are indefficient in comparsion wiht high-order finite differences. With the use of summation-by-parts (SBP) operators and the SAT penalty method (simultaneous approximation term) it is possible to couple unstructured finite volume methods with high-order finite difference methods in an accurate and stable way. The couple method is more efficient than the unstructured method alone. Another advantage of the SBP and SAT method is that it is possible to prove strict stability, meaning that the semi-discrete solution dissipates energy at a slightly faster rate than the continuous solution so that the error remains bounded in time, which is particulary useful for long time computations.
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| 45. |
- O´Reilly, Ossian, et al.
(författare)
-
Earthquake Rupture dynamics in complex geometries using coupled high-order finite difference methods and finite volume methods
- 2012
-
Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- We present a 2-D multi-block method for earthquake rupture dynamics in complex geometries using summation-byparts (SBP) high-order finite differences on structured grids coupled to nite volume methods on unstructured meshes. The node-centered nite volume method is used on unstructured triangular meshes to resolve earthquake ruptures propagating along non-planar faults with complex geometrical features. The unstructured meshes discretize the fault geometry only in the vicinity of the faults and have collocated nodes on the fault boundaries. Away from faults, where no complex geometry is present, the seismic waves emanating from the earthquake rupture are resolved using the high-order finite difference method on coarsened structured grids, improving the computational efficiency while maintaining the accuracy of the method.In order for the SBP high-order nite difference method to communicate with the node-centered finite volume method in a stable manner, interface conditions are imposed using the simultaneous approximation term (SAT) penalty method. In the SAT method the interface conditions and boundary conditions are imposed in a weak manner.Fault interface conditions (rate-and-state friction) are also imposed in a provably stable manner using the SAT method. Another advantage of the SAT method is the ability to impose multiple boundary conditions at a single boundary node, e.g. at the triple junction of a branching fault.The accuracy and stability of the numerical implementation are veried using the method of manufactured solutions and against other numerical implementations. To demonstrate the potential of the method, we simulate an earthquake rupture propagating in a nonplanar fault geometry resolved with unstructured meshes in the fault zone and structured grids in the far-eld.
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| 46. |
- O´Reilly, Ossian, et al.
(författare)
-
Earthquake Rupture Dynamics in Complex Geometries using Coupled Summation-By-Parts High-order Finite Difference Methods and Node-Centered Finite Volume Methods
- 2012
-
Ingår i: Souther California Earthquacke Center, Annual Meeting.
-
Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- We present a 2-D multi-block method for earthquake rupture dynamics in complex geometries using summation-byparts (SBP) high-order nite di-erences on structured grids coupled to nite volume methods on unstructured meshes. The node-centered nite volume method is used on unstructured triangular meshes to resolve earthquake ruptures propagating along nonplanar faults with complex geometrical features. The unstructured meshes discretize the fault geometry only in the vicinity of the faults and have collocated nodes on the fault boundaries. Away from faults, where no complex geometry is present, the seismic waves emanating from the earthquake rupture are resolved using the high-order nite di-erence method on coarsened structured grids, improving the computational e ciency while maintaining the accuracy of the method.In order for the SBP high-order nite di-erence method to communicate with the node-centered nite volume method in a stable manner, interface conditions are imposed using the simultaneous approximation term (SAT) penalty method. In the SAT method the interface conditions and boundary conditions are imposed in a weak manner.Fault interface conditions (rate-and-state friction) are also imposed in a provably stable manner using the SAT method. Another advantage of the SAT method is the ability to impose multiple boundary conditions at a single boundary node, e.g., at the triple junction of a branching fault.The accuracy and stability of the numerical implementation are veried using the method of manufactured solutions and against other numerical implementations. To demonstrate the potential of the method, we simulate an earthquake rupture propagating in a nonplanar fault geometry resolved with unstructured meshes in the fault zone and structured grids in the far-eld.
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| 47. |
- O´Reilly, Ossian, et al.
(författare)
-
High-order finite difference methods for eartquake rupture dynamics in complex geometries
- 2010
-
Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Unstructured grid methods are well suited for earthquake problems in complex geometries, such as non-planar and branching faults. Unfortunately they are inefficient in comparisioin with high-order finite difference. With the use of summertion-by-parts (SBP) operators and the SAT penalty method (simultaneous approximation term) it is possible to couple unstructuren finite volume methods wiht high order finite difference methods in an accurate and stable way. The coupled methods is more efficient than the unstructured method alone. Another advantage of the SBP and SAT method is that it is possible to prove strict stability, meaning that the semi-discrete solution dissipates energy at a slightly faster rate than the continuous solution so that the error remains bounded in time, which is particulary useful for long time computations.
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| 48. |
- O´Reilly, Ossian, et al.
(författare)
-
Simulation of Earthquake Rupture Dynamics in Complex Geometries Using Coupled Finite Difference and Finite Volume Methods
- 2013
-
Rapport (övrigt vetenskapligt/konstnärligt)abstract
- A numerical method suitable for wave propagation problems in complex geometries is developed for simulating dynamic earthquake ruptures with realistic friction laws. The numerical method couples an unstructured, node-centered finite volume method to a structured, high order finite difference method. In this work we our focus attention on 2-D antiplane shear problems. The finite volume method is used on unstructured triangular meshes to resolve earthquake ruptures propagating along a nonplanar fault. Outside the small region containing the geometrically complex fault, a high order finite difference method, having superior numerical accuracy, is used on a structured grid.The finite difference method is coupled weakly to the finite volume method along interfaces of collocated grid points. Both methods are on summation-by-parts form. The simultaneous approximation term method is used to weakly enforce the interface conditions. At fault interfaces, fault strength is expressed as a nonlinear function of sliding velocity (the jump in particle velocity across the fault) and a state variable capturing the history dependence of frictional resistance. Energy estimates are used to prove that both types of interface conditions are imposed in a stable manner.Stability and accuracy of the numerical implementation are verified through numerical experiments, and efficiency of the hybrid approach is confirmed through grid coarsening tests. Finally, the method is used to study earthquake rupture propagation along the margins of a volcanic plug.
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| 49. |
- O’Reilly, Ossian, et al.
(författare)
-
Energy stable and high-order-accurate finite difference methods on staggered grids
- 2016
-
Rapport (övrigt vetenskapligt/konstnärligt)abstract
- For wave propagation over distances of many wavelengths, high-order finite difference methods on staggered grids are widely used due to their excellent dispersion properties. However, the enforcement of boundary conditions in a stable manner and treatment of interface problems with discontinuous coefficients usually pose many challenges. In this work, we construct a provably stable and high-order-accurate finite difference method on staggered grids that can be applied to a broad class of boundary and interface problems. The staggered grid difference operators are in summation-by-parts form and when combined with a weak enforcement of the boundary conditions, lead to an energy stable method on multiblock grids. The general applicability of the method is demonstrated by simulating an explosive acoustic source, generating waves reflecting against a free surface and material discontinuity.
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| 50. |
- O'Reilly, Ossian, et al.
(författare)
-
Energy stable and high-order-accurate finite difference methods on staggered grids
- 2017
-
Ingår i: Journal of Computational Physics. - : Academic Press. - 0021-9991 .- 1090-2716. ; 346, s. 572-589
-
Tidskriftsartikel (refereegranskat)abstract
- For wave propagation over distances of many wavelengths, high-order finite difference methods on staggered grids are widely used due to their excellent dispersion properties. However, the enforcement of boundary conditions in a stable manner and treatment of interface problems with discontinuous coefficients usually pose many challenges. In this work, we construct a provably stable and high-order-accurate finite difference method on staggered grids that can be applied to a broad class of boundary and interface problems. The staggered grid difference operators are in summation-by-parts form and when combined with a weak enforcement of the boundary conditions, lead to an energy stable method on multiblock grids. The general applicability of the method is demonstrated by simulating an explosive acoustic source, generating waves reflecting against a free surface and material discontinuity.
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