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- 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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- Kehoe, Laura, et al.
(författare)
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Make EU trade with Brazil sustainable
- 2019
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 364:6438, s. 341-
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 6. |
- Tinetti, G., et al.
(författare)
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A chemical survey of exoplanets with ARIEL
- 2018
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Ingår i: Experimental Astronomy. - : Springer Science and Business Media LLC. - 0922-6435 .- 1572-9508. ; 46:1, s. 135-209
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Tidskriftsartikel (refereegranskat)abstract
- Thousands of exoplanets have now been discovered with a huge range of masses, sizes and orbits: from rocky Earth-like planets to large gas giants grazing the surface of their host star. However, the essential nature of these exoplanets remains largely mysterious: there is no known, discernible pattern linking the presence, size, or orbital parameters of a planet to the nature of its parent star. We have little idea whether the chemistry of a planet is linked to its formation environment, or whether the type of host star drives the physics and chemistry of the planet’s birth, and evolution. ARIEL was conceived to observe a large number (~1000) of transiting planets for statistical understanding, including gas giants, Neptunes, super-Earths and Earth-size planets around a range of host star types using transit spectroscopy in the 1.25–7.8 μm spectral range and multiple narrow-band photometry in the optical. ARIEL will focus on warm and hot planets to take advantage of their well-mixed atmospheres which should show minimal condensation and sequestration of high-Z materials compared to their colder Solar System siblings. Said warm and hot atmospheres are expected to be more representative of the planetary bulk composition. Observations of these warm/hot exoplanets, and in particular of their elemental composition (especially C, O, N, S, Si), will allow the understanding of the early stages of planetary and atmospheric formation during the nebular phase and the following few million years. ARIEL will thus provide a representative picture of the chemical nature of the exoplanets and relate this directly to the type and chemical environment of the host star. ARIEL is designed as a dedicated survey mission for combined-light spectroscopy, capable of observing a large and well-defined planet sample within its 4-year mission lifetime. Transit, eclipse and phase-curve spectroscopy methods, whereby the signal from the star and planet are differentiated using knowledge of the planetary ephemerides, allow us to measure atmospheric signals from the planet at levels of 10–100 part per million (ppm) relative to the star and, given the bright nature of targets, also allows more sophisticated techniques, such as eclipse mapping, to give a deeper insight into the nature of the atmosphere. These types of observations require a stable payload and satellite platform with broad, instantaneous wavelength coverage to detect many molecular species, probe the thermal structure, identify clouds and monitor the stellar activity. The wavelength range proposed covers all the expected major atmospheric gases from e.g. H2O, CO2, CH4 NH3, HCN, H2S through to the more exotic metallic compounds, such as TiO, VO, and condensed species. Simulations of ARIEL performance in conducting exoplanet surveys have been performed – using conservative estimates of mission performance and a full model of all significant noise sources in the measurement – using a list of potential ARIEL targets that incorporates the latest available exoplanet statistics. The conclusion at the end of the Phase A study, is that ARIEL – in line with the stated mission objectives – will be able to observe about 1000 exoplanets depending on the details of the adopted survey strategy, thus confirming the feasibility of the main science objectives.
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- Ladds, Marcus J. G. W., et al.
(författare)
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A DHODH inhibitor increases p53 synthesis and enhances tumor cell killing by p53 degradation blockage
- 2018
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- The development of non-genotoxic therapies that activate wild-type p53 in tumors is of great interest since the discovery of p53 as a tumor suppressor. Here we report the identification of over 100 small-molecules activating p53 in cells. We elucidate the mechanism of action of a chiral tetrahydroindazole (HZ00), and through target deconvolution, we deduce that its active enantiomer (R)-HZ00, inhibits dihydroorotate dehydrogenase (DHODH). The chiral specificity of HZ05, a more potent analog, is revealed by the crystal structure of the (R)-HZ05/DHODH complex. Twelve other DHODH inhibitor chemotypes are detailed among the p53 activators, which identifies DHODH as a frequent target for structurally diverse compounds. We observe that HZ compounds accumulate cancer cells in S-phase, increase p53 synthesis, and synergize with an inhibitor of p53 degradation to reduce tumor growth in vivo. We, therefore, propose a strategy to promote cancer cell killing by p53 instead of its reversible cell cycle arresting effect.
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| 8. |
- Saygi, B., et al.
(författare)
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Reduced transition probabilities along the yrast line in W-166
- 2017
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Ingår i: Physical Review C. - : American Physical Society. - 2469-9985 .- 2469-9993. ; 96:2
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Tidskriftsartikel (refereegranskat)abstract
- Lifetimes of excited states in the yrast band of the neutron-deficient nuclide W-166 have been measured utilizing the DPUNS plunger device at the target position of the JUROGAM II gamma-ray spectrometer in conjunction with the RITU gas-filled separator and the GREAT focal-plane spectrometer. Excited states in W-166 were populated in the Mo-92(Kr-78, 4p) reaction at a bombarding energy of 380 MeV. The measurements reveal a low value for the ratio of reduced transitions probabilities for the lowest-lying transitions B(E2; 4(+)-> 2(+)) / B(E2; 2(+)-> 0(+)) = 0.33(5), compared with the expected ratio for an axially deformed rotor (B-4/2 = 1.43).
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| 9. |
- Doncel, Maria, et al.
(författare)
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Lifetime measurements of excited states in W-162 and W-164 and the evolution of collectivity in rare-earth nuclei
- 2017
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Ingår i: Physical Review C. - : American Physical Society. - 2469-9985 .- 2469-9993. ; 95:4
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Tidskriftsartikel (refereegranskat)abstract
- Lifetimes of the first excited 2(+) states in the extremely neutron- deficient W-162 and W-164 nuclei have been measured using the recoil distance Doppler shift technique. Experimental B(E2) data for the isotopic chains of hafnium, tungsten, and osmium, from the midshell region near the beta-stability line towards the N = 82 closed shell and the most neutron-deficient nuclides, are compared with predictions of nuclear deformations and 2(1)(+) -> 0(g.s)(.+) reduced transition strengths from different classes of state-of-the-art theoretical model calculations. The results reveal striking differences and deficiencies in the predictive power of current nuclear structure models.
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| 10. |
- Li, Hongjie, et al.
(författare)
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Recoil-decay tagging spectroscopy of W-162(74)88
- 2015
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Ingår i: Physical Review C. Nuclear Physics. - 0556-2813 .- 1089-490X. ; 92:1
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Tidskriftsartikel (refereegranskat)abstract
- Excited states in the highly neutron-deficient nucleus W-162 have been investigated via the Mo-92(Kr-78, 2 alpha) W-162 reaction. Prompt gamma rays were detected by the JUROGAM II high-purity germanium detector array and the recoiling fusion-evaporation products were separated by the recoil ion transport unit (RITU) gas-filled recoil separator and identified with the gamma recoil electron alpha tagging (GREAT) spectrometer at the focal plane of RITU. gamma rays from W-162 were identified uniquely using mother-daughter and mother-daughter-granddaughter alpha-decay correlations. The observation of a rotational-like ground-state band is interpreted within the framework of total Routhian surface (TRS) calculations, which suggest an axially symmetric ground-state shape with a gamma-soft minimum at beta(2) approximate to 0.15. Quasiparticle alignment effects are discussed based on cranked shell model calculations. New measurements of the W-162 ground-state alpha-decay energy and half-life were also performed. The observed alpha-decay energy agrees with previous measurements. The half-life of W-162 was determined to be t(1/2) = 990(30) ms. This value deviates significantly from the currently adopted value of t(1/2) = 1360(70) ms. In addition, the alpha-decay energy and half-life of Os-166 were measured and found to agree with the adopted values.
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