| 1. |
- Weinstein, John N., et al.
(author)
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The cancer genome atlas pan-cancer analysis project
- 2013
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In: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 45:10, s. 1113-1120
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Research review (peer-reviewed)abstract
- The Cancer Genome Atlas (TCGA) Research Network has profiled and analyzed large numbers of human tumors to discover molecular aberrations at the DNA, RNA, protein and epigenetic levels. The resulting rich data provide a major opportunity to develop an integrated picture of commonalities, differences and emergent themes across tumor lineages. The Pan-Cancer initiative compares the first 12 tumor types profiled by TCGA. Analysis of the molecular aberrations and their functional roles across tumor types will teach us how to extend therapies effective in one cancer type to others with a similar genomic profile. © 2013 Nature America, Inc. All rights reserved.
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| 2. |
- Everitt, Aaron R, et al.
(author)
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Defining the range of pathogens susceptible to Ifitm3 restriction using a knockout mouse model
- 2013
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In: PLOS ONE. - : Public Library of Science. - 1932-6203. ; 8:11, s. e80723-e80723
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Journal article (peer-reviewed)abstract
- The interferon-inducible transmembrane (IFITM) family of proteins has been shown to restrict a broad range of viruses in vitro and in vivo by halting progress through the late endosomal pathway. Further, single nucleotide polymorphisms (SNPs) in its sequence have been linked with risk of developing severe influenza virus infections in humans. The number of viruses restricted by this host protein has continued to grow since it was first demonstrated as playing an antiviral role; all of which enter cells via the endosomal pathway. We therefore sought to test the limits of antimicrobial restriction by Ifitm3 using a knockout mouse model. We showed that Ifitm3 does not impact on the restriction or pathogenesis of bacterial (Salmonella typhimurium, Citrobacter rodentium, Mycobacterium tuberculosis) or protozoan (Plasmodium berghei) pathogens, despite in vitro evidence. However, Ifitm3 is capable of restricting respiratory syncytial virus (RSV) in vivo either through directly restricting RSV cell infection, or by exerting a previously uncharacterised function controlling disease pathogenesis. This represents the first demonstration of a virus that enters directly through the plasma membrane, without the need for the endosomal pathway, being restricted by the IFITM family; therefore further defining the role of these antiviral proteins.
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| 3. |
- Kane, Gordon, et al.
(author)
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Baryogenesis from a modulus dominated universe
- 2020
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In: Journal of Cosmology and Astroparticle Physics. - : IOP Publishing. - 1475-7516. ; :02
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Journal article (peer-reviewed)abstract
- String/ M-theory compactifications predict the existence of a modulus field with a mass of 100-10000TeV. Its decay at MeV-temperatures generates large amounts of entropy and washes out any previously produced baryon asymmetry. We describe how the baryon asymmetry can be (re)generated by the modulus decay. The mechanism relates the smallness of the asymmetry to the hierarchy between the Planck- and the Fermi-scale.
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| 4. |
- Kane, Gordon, et al.
(author)
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Deriving the inflaton in compactified M-theory with a de Sitter vacuum
- 2019
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In: Physical Review D. - 2470-0010 .- 2470-0029. ; 100:6
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Journal article (peer-reviewed)abstract
- Compactifying M-theory on a manifold of G2 holonomy gives a UV complete 4D theory. It is supersymmetric, with soft supersymmetry breaking via gaugino condensation that simultaneously stabilizes all moduli and generates a hierarchy between the Planck and the Fermi scale. It generically has gauge matter, chiral fermions, and several other important features of our world. Here we show that the theory also contains a successful inflaton, which is a linear combination of moduli closely aligned with the overall volume modulus of the compactified G2 manifold. The scheme does not rely on ad hoc assumptions, but derives from an effective quantum theory of gravity. Inflation arises near an inflection point in the potential which can be deformed into a local minimum. This implies that a de Sitter vacuum can occur in the moduli potential even without uplifting. Generically present charged hidden sector matter generates a de Sitter vacuum as well.
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| 5. |
- Lattanzi, Massimiliano, et al.
(author)
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Cornering (quasi) degenerate neutrinos with cosmology
- 2020
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In: Journal of High Energy Physics (JHEP). - 1126-6708 .- 1029-8479. ; :10
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Journal article (peer-reviewed)abstract
- In light of the improved sensitivities of cosmological observations, we examine the status of quasi-degenerate neutrino mass scenarios. Within the simplest extension of the standard cosmological model with massive neutrinos, we find that quasi-degenerate neutrinos are severely constrained by present cosmological data and neutrino oscillation experiments. We find that Planck 2018 observations of cosmic microwave background (CMB) anisotropies disfavour quasi-degenerate neutrino masses at 2.4 Gaussian sigma 's, while adding baryon acoustic oscillations (BAO) data brings the rejection to 5.9 sigma 's. The highest statistical significance with which one would be able to rule out quasi-degeneracy would arise if the sum of neutrino masses is Sigma m(v) = 60 meV (the minimum allowed by neutrino oscillation experiments); indeed a sensitivity of 15 meV, as expected from a combination of future cosmological probes, would further improve the rejection level up to 17 sigma. We discuss the robustness of these projections with respect to assumptions on the underlying cosmological model, and also compare them with bounds from beta decay endpoint and neutrinoless double beta decay studies.
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| 6. |
- Schweinsberg, Martin, et al.
(author)
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Same data, different conclusions : Radical dispersion in empirical results when independent analysts operationalize and test the same hypothesis
- 2021
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In: Organizational Behavior and Human Decision Processes. - : Elsevier BV. - 0749-5978 .- 1095-9920. ; 165, s. 228-249
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Journal article (peer-reviewed)abstract
- In this crowdsourced initiative, independent analysts used the same dataset to test two hypotheses regarding the effects of scientists' gender and professional status on verbosity during group meetings. Not only the analytic approach but also the operationalizations of key variables were left unconstrained and up to individual analysts. For instance, analysts could choose to operationalize status as job title, institutional ranking, citation counts, or some combination. To maximize transparency regarding the process by which analytic choices are made, the analysts used a platform we developed called DataExplained to justify both preferred and rejected analytic paths in real time. Analyses lacking sufficient detail, reproducible code, or with statistical errors were excluded, resulting in 29 analyses in the final sample. Researchers reported radically different analyses and dispersed empirical outcomes, in a number of cases obtaining significant effects in opposite directions for the same research question. A Boba multiverse analysis demonstrates that decisions about how to operationalize variables explain variability in outcomes above and beyond statistical choices (e.g., covariates). Subjective researcher decisions play a critical role in driving the reported empirical results, underscoring the need for open data, systematic robustness checks, and transparency regarding both analytic paths taken and not taken. Implications for orga-nizations and leaders, whose decision making relies in part on scientific findings, consulting reports, and internal analyses by data scientists, are discussed.
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