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- 2019
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Tidskriftsartikel (refereegranskat)
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| 2. |
- 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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| 3. |
- Andreasson, Jakob, 1975, et al.
(författare)
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Electron-lattice interactions in the perovskite LaFe0.5Cr0.5O3 characterized by optical spectroscopy and LDA plus U calculations
- 2009
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Ingår i: Physical Review B. Condensed Matter and Materials Physics. - 1098-0121 .- 1550-235X .- 2469-9950 .- 2469-9969. ; 80:7, s. 075103-
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Tidskriftsartikel (refereegranskat)abstract
- We use resonance Raman scattering (incident photon energies between 1.8 and 4.13 eV), LDA+U calculations, spectroscopic ellipsometry, and oblique IR reflectivity to characterize the strong electron-phonon interactions in the disordered perovskite LaFe0.5Cr0.5O3. When the photon energy coincides with a Cr to Fe Mott-Hubbard transfer gap around 2.4 eV the electron-phonon interaction is manifested by a Franck-Condon effect with exceptional first-and higher order scattering of a local oxygen breathing mode. At higher incident energies we observe a superposition of Franck-Condon scattering and Frohlich interaction induced infrared active longitudinal optical two-phonon scattering activated mainly by O to Fe charge transfer. Our results establish LaFe0.5Cr0.5O3 as a model compound for research on electron-phonon interactions in strongly correlated complex systems and show that Franck-Condon scattering in complex solids is not limited to Jahn-Teller active compounds.
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| 4. |
- Andreoni, Igor, et al.
(författare)
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Target-of-opportunity Observations of Gravitational-wave Events with Vera C. Rubin Observatory
- 2022
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Ingår i: Astrophysical Journal Supplement Series. - : American Astronomical Society. - 0067-0049 .- 1538-4365. ; 260:1
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Tidskriftsartikel (refereegranskat)abstract
- The discovery of the electromagnetic counterpart to the binary neutron star (NS) merger GW170817 has opened the era of gravitational-wave multimessenger astronomy. Rapid identification of the optical/infrared kilonova enabled a precise localization of the source, which paved the way to deep multiwavelength follow-up and its myriad of related science results. Fully exploiting this new territory of exploration requires the acquisition of electromagnetic data from samples of NS mergers and other gravitational-wave sources. After GW170817, the frontier is now to map the diversity of kilonova properties and provide more stringent constraints on the Hubble constant, and enable new tests of fundamental physics. The Vera C. Rubin Observatory's Legacy Survey of Space and Time can play a key role in this field in the 2020s, when an improved network of gravitational-wave detectors is expected to reach a sensitivity that will enable the discovery of a high rate of merger events involving NSs (∼tens per year) out to distances of several hundred megaparsecs. We design comprehensive target-of-opportunity observing strategies for follow-up of gravitational-wave triggers that will make the Rubin Observatory the premier instrument for discovery and early characterization of NS and other compact-object mergers, and yet unknown classes of gravitational-wave events.
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| 5. |
- Antoniou, Antonis C., et al.
(författare)
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Common alleles at 6q25.1 and 1p11.2 are associated with breast cancer risk for BRCA1 and BRCA2 mutation carriers
- 2011
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Ingår i: Human Molecular Genetics. - : Oxford University Press (OUP). - 0964-6906 .- 1460-2083. ; 20:16, s. 3304-3321
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Tidskriftsartikel (refereegranskat)abstract
- Two single nucleotide polymorphisms (SNPs) at 6q25.1, near the ESR1 gene, have been implicated in the susceptibility to breast cancer for Asian (rs2046210) and European women (rs9397435). A genome-wide association study in Europeans identified two further breast cancer susceptibility variants: rs11249433 at 1p11.2 and rs999737 in RAD51L1 at 14q24.1. Although previously identified breast cancer susceptibility variants have been shown to be associated with breast cancer risk for BRCA1 and BRCA2 mutation carriers, the involvement of these SNPs to breast cancer susceptibility in mutation carriers is currently unknown. To address this, we genotyped these SNPs in BRCA1 and BRCA2 mutation carriers from 42 studies from the Consortium of Investigators of Modifiers of BRCA1/2. In the analysis of 14 123 BRCA1 and 8053 BRCA2 mutation carriers of European ancestry, the 6q25.1 SNPs (r(2) = 0.14) were independently associated with the risk of breast cancer for BRCA1 mutation carriers [ hazard ratio (HR) = 1.17, 95% confidence interval (CI): 1.11-1.23, P-trend = 4.5 x 10(-9) for rs2046210; HR = 1.28, 95% CI: 1.18-1.40, P-trend = 1.3 x 10(-8) for rs9397435], but only rs9397435 was associated with the risk for BRCA2 carriers (HR = 1.14, 95% CI: 1.01-1.28, P-trend = 0.031). SNP rs11249433 (1p11.2) was associated with the risk of breast cancer for BRCA2 mutation carriers (HR = 1.09, 95% CI: 1.02-1.17, P-trend = 0.015), but was not associated with breast cancer risk for BRCA1 mutation carriers (HR = 0.97, 95% CI: 0.92-1.02, P-trend = 0.20). SNP rs999737 (RAD51L1) was not associated with breast cancer risk for either BRCA1 or BRCA2 mutation carriers (P-trend = 0.27 and 0.30, respectively). The identification of SNPs at 6q25.1 associated with breast cancer risk for BRCA1 mutation carriers will lead to a better understanding of the biology of tumour development in these women.
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| 6. |
- Bradter, Ute, et al.
(författare)
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Can opportunistically collected Citizen Science data fill a data gap for habitat suitability models of less common species?
- 2018
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Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 9, s. 1667-1678
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Tidskriftsartikel (refereegranskat)abstract
- 1. Opportunistically collected species observations contributed by volunteer reporters are increasingly available for species and regions for which systematically collected data are not available. However, it is unclear if they are suitable to produce reliable habitat suitability models (HSMs), and hence if the species-habitat relationships found and habitat suitability maps produced can be used with confidence to advice conservation management and address basic and applied research questions.2. We evaluated HSMs with opportunistically collected observations against HSMs with systematically collected observations. We enhanced the opportunistically collected presence-only data by adding inferred species absences. To obtain inferred absences, we asked individual reporters about their identification skills and if they reported certain species consistently and combined this information with their observations. We evaluated several HSM methods using a forest bird species, Siberian jay (Perisoreus infaustus), in Sweden: logistic regression with inferred absences, two versions of MaxEnt, a model combining presence-absence with presence-only observations and a Bayesian site-occupancy-detection model.3. All HSM methods produced nationwide habitat suitability maps of Siberian jay that agreed well with systematically collected observations (AUC: 086-0.88) and were very similar to a habitat suitability map produced from the HSM with systematically collected observations (Spearman rho: 0.94-0.98). At finer geographical scales there were differences among methods.4. At finer scale, the resulting habitat suitability maps from logistic regression with inferred absences agreed better with results from systematically collected observations than other methods. The species-habitat relationships found with logistic regression also agreed well with those found from systematically collected data and with prior expectations based on the species ecology.5. Synthesis and application. For many regions and species, systematically collected data are not available. By using inferred absences from high-quality, opportunistically collected contributions of few very active reporters in logistic regression we obtained HSMs that produced results similar to those from a systematic survey. Adding high-quality inferred absences to opportunistically collected data is likely possible for many less common species across various organism groups. Well-performing HSMs are important to facilitate applications such as spatial conservation planning and prioritization, monitoring of invasive species, understanding species habitat requirements or climate change studies.
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| 7. |
- Bradter, Ute, et al.
(författare)
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Habitat suitability models based on opportunistic citizen science data: Evaluating forecasts from alternative methods versus an individual-based model
- 2021
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Ingår i: Diversity and Distributions. - : Wiley. - 1366-9516 .- 1472-4642. ; 27, s. 2397-2411
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Tidskriftsartikel (refereegranskat)abstract
- Aim To evaluate the utility of opportunistic data from citizen science programmes for forecasting species distributions against forecasts with a model of individual-based population dynamics. Location Sweden. Methods We evaluated whether alternative methods for building habitat suitability models (HSMs) based on opportunistic data from citizen science programmes produced forecasts that were consistent with forecasts from two benchmark models: (1) a HSM based on data from systematic monitoring and (2) an individual-based model for spatially explicit population dynamics based on empirical demographic and movement data. We forecasted population numbers and habitat suitability for three realistic, future forest landscapes for a forest bird, the Siberian jay (Perisoreus infaustus). We ranked simulated forest landscapes with respect to their benefits to Siberian jays for each modelling method and compared the agreement of the rankings among methods. Results Forecasts based on our two benchmark models were consistent with each other and with expectations based on the species' ecology. Forecasts from logistic regression models based on opportunistic data were consistent with the benchmark models if species detections were combined with high-quality inferred absences derived via retrospective interviews with experienced "super-reporters." In contrast, forecasts with three other widely used methods were inconsistent with the benchmark models, sometimes with misleading rankings of future scenarios. Main conclusions Our critical evaluation of alternative HSMs against a spatially explicit IBM demonstrates that information on species absences critically improves forecasts of species distributions using opportunistic data from citizen science programmes. Moreover, high-quality information on species absences can be retrospectively inferred from surveys of the consistency of reporting of individual species and the identification skills of participating reporters. We recommend that citizen science projects incorporate procedures to evaluate reporting behaviour. Inferred absences may be especially useful for improving forecasts for species and regions poorly covered by systematic monitoring schemes.
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| 8. |
- Fabritius, Henna, et al.
(författare)
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Estimation of metapopulation colonization rates from disturbance history and occurrence-pattern data
- 2019
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Ingår i: Ecology. - : Wiley. - 0012-9658 .- 1939-9170. ; 100
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Tidskriftsartikel (refereegranskat)abstract
- Occurrence patterns of many sessile species in dynamic landscapes are not in equilibrium due to their slow rates of metapopulation colonization and extinction. Colonization-extinction data enable the estimation of colonization rates for such species, but collecting the necessary data may require long waiting times between sampling years. Methods for estimating colonization rates of nonequilibrium metapopulations from single occurrence-pattern data have so far relied on additional data on patch ages and on past patch connectivities. We present an approach where metapopulation colonization rates are estimated from occurrence-pattern data and from disturbance history data that inform of past patch dynamics and that can be collected together with occurrence-pattern data. We estimated parameter values regulating patch and metapopulation dynamics by simulating patch network and metapopulation histories that result in present-like patch network configurations and metapopulation occurrence patterns. We tested our approach using occurrence-pattern data of the epiphytic lichen Lobaria pulmonaria in Fennoscandian forests, and fire-scar data that inform of the 400-yr history of fires and host tree dynamics in the same landscapes. The estimated model parameters were similar to estimates obtained using colonization-extinction data. The projected L. pulmonaria occupancy into the future also agreed with the respective projections that were made using the model estimated from colonization-extinction data. Our approach accelerates the estimation of metapopulation colonization rates for sessile species that are not in metapopulation equilibrium with the current landscape structure.
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| 9. |
- Hollestelle, Antoinette, et al.
(författare)
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No clinical utility of KRAS variant rs61764370 for ovarian or breast cancer
- 2016
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Ingår i: Gynecologic Oncology. - : Elsevier BV. - 0090-8258 .- 1095-6859. ; 141:2, s. 386-401
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Tidskriftsartikel (refereegranskat)abstract
- Objective Clinical genetic testing is commercially available for rs61764370, an inherited variant residing in a KRAS 3′ UTR microRNA binding site, based on suggested associations with increased ovarian and breast cancer risk as well as with survival time. However, prior studies, emphasizing particular subgroups, were relatively small. Therefore, we comprehensively evaluated ovarian and breast cancer risks as well as clinical outcome associated with rs61764370. Methods Centralized genotyping and analysis were performed for 140,012 women enrolled in the Ovarian Cancer Association Consortium (15,357 ovarian cancer patients; 30,816 controls), the Breast Cancer Association Consortium (33,530 breast cancer patients; 37,640 controls), and the Consortium of Modifiers of BRCA1 and BRCA2 (14,765 BRCA1 and 7904 BRCA2 mutation carriers). Results We found no association with risk of ovarian cancer (OR = 0.99, 95% CI 0.94-1.04, p = 0.74) or breast cancer (OR = 0.98, 95% CI 0.94-1.01, p = 0.19) and results were consistent among mutation carriers (BRCA1, ovarian cancer HR = 1.09, 95% CI 0.97-1.23, p = 0.14, breast cancer HR = 1.04, 95% CI 0.97-1.12, p = 0.27; BRCA2, ovarian cancer HR = 0.89, 95% CI 0.71-1.13, p = 0.34, breast cancer HR = 1.06, 95% CI 0.94-1.19, p = 0.35). Null results were also obtained for associations with overall survival following ovarian cancer (HR = 0.94, 95% CI 0.83-1.07, p = 0.38), breast cancer (HR = 0.96, 95% CI 0.87-1.06, p = 0.38), and all other previously-reported associations. Conclusions rs61764370 is not associated with risk of ovarian or breast cancer nor with clinical outcome for patients with these cancers. Therefore, genotyping this variant has no clinical utility related to the prediction or management of these cancers.
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| 10. |
- Huerta, E. A., et al.
(författare)
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Enabling real-time multi-messenger astrophysics discoveries with deep learning
- 2019
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Ingår i: Nature reviews physics. - : Springer Science and Business Media LLC. - 2522-5820. ; 1:10, s. 600-608
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Forskningsöversikt (refereegranskat)abstract
- Multi-messenger astrophysics is a fast-growing, interdisciplinary field that combines data, which vary in volume and speed of data processing, from many different instruments that probe the Universe using different cosmic messengers: electromagnetic waves, cosmic rays, gravitational waves and neutrinos. In this Expert Recommendation, we review the key challenges of real-time observations of gravitational wave sources and their electromagnetic and astroparticle counterparts, and make a number of recommendations to maximize their potential for scientific discovery. These recommendations refer to the design of scalable and computationally efficient machine learning algorithms; the cyber-infrastructure to numerically simulate astrophysical sources, and to process and interpret multi-messenger astrophysics data; the management of gravitational wave detections to trigger real-time alerts for electromagnetic and astroparticle follow-ups; a vision to harness future developments of machine learning and cyber-infrastructure resources to cope with the big-data requirements; and the need to build a community of experts to realize the goals of multi-messenger astrophysics. A group of experts suggests ways in which deep learning can be used to enhance the potential for discovery in multi-messenger astrophysics.
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