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- Clark, Andrew G., et al.
(author)
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Evolution of genes and genomes on the Drosophila phylogeny
- 2007
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 450:7167, s. 203-218
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Journal article (peer-reviewed)abstract
- Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.
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- Stanaway, Jeffrey D., et al.
(author)
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Global, regional, and national comparative risk assessment of 84 behavioural, environmental and occupational, and metabolic risks or clusters of risks for 195 countries and territories, 1990-2017: A systematic analysis for the Global Burden of Disease Study 2017
- 2018
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In: The Lancet. - 1474-547X .- 0140-6736. ; 392:10159, s. 1923-1994
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Journal article (peer-reviewed)abstract
- Background The Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2017 comparative risk assessment (CRA) is a comprehensive approach to risk factor quantification that offers a useful tool for synthesising evidence on risks and risk-outcome associations. With each annual GBD study, we update the GBD CRA to incorporate improved methods, new risks and risk-outcome pairs, and new data on risk exposure levels and risk- outcome associations. Methods We used the CRA framework developed for previous iterations of GBD to estimate levels and trends in exposure, attributable deaths, and attributable disability-adjusted life-years (DALYs), by age group, sex, year, and location for 84 behavioural, environmental and occupational, and metabolic risks or groups of risks from 1990 to 2017. This study included 476 risk-outcome pairs that met the GBD study criteria for convincing or probable evidence of causation. We extracted relative risk and exposure estimates from 46 749 randomised controlled trials, cohort studies, household surveys, census data, satellite data, and other sources. We used statistical models to pool data, adjust for bias, and incorporate covariates. Using the counterfactual scenario of theoretical minimum risk exposure level (TMREL), we estimated the portion of deaths and DALYs that could be attributed to a given risk. We explored the relationship between development and risk exposure by modelling the relationship between the Socio-demographic Index (SDI) and risk-weighted exposure prevalence and estimated expected levels of exposure and risk-attributable burden by SDI. Finally, we explored temporal changes in risk-attributable DALYs by decomposing those changes into six main component drivers of change as follows: (1) population growth; (2) changes in population age structures; (3) changes in exposure to environmental and occupational risks; (4) changes in exposure to behavioural risks; (5) changes in exposure to metabolic risks; and (6) changes due to all other factors, approximated as the risk-deleted death and DALY rates, where the risk-deleted rate is the rate that would be observed had we reduced the exposure levels to the TMREL for all risk factors included in GBD 2017.
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- Santangelo, James S., et al.
(author)
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Global urban environmental change drives adaptation in white clover
- 2022
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In: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 375
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Journal article (peer-reviewed)abstract
- Urbanization transforms environments in ways that alter biological evolution. We examined whether urban environmental change drives parallel evolution by sampling 110,019 white clover plants from 6169 populations in 160 cities globally. Plants were assayed for a Mendelian antiherbivore defense that also affects tolerance to abiotic stressors. Urban-rural gradients were associated with the evolution of clines in defense in 47% of cities throughout the world. Variation in the strength of clines was explained by environmental changes in drought stress and vegetation cover that varied among cities. Sequencing 2074 genomes from 26 cities revealed that the evolution of urban-rural dines was best explained by adaptive evolution, but the degree of parallel adaptation varied among cities. Our results demonstrate that urbanization leads to adaptation at a global scale.
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- Lindblad-Toh, Kerstin, et al.
(author)
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Genome sequence, comparative analysis and haplotype structure of the domestic dog.
- 2005
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In: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 438:7069, s. 803-19
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Journal article (peer-reviewed)abstract
- Here we report a high-quality draft genome sequence of the domestic dog (Canis familiaris), together with a dense map of single nucleotide polymorphisms (SNPs) across breeds. The dog is of particular interest because it provides important evolutionary information and because existing breeds show great phenotypic diversity for morphological, physiological and behavioural traits. We use sequence comparison with the primate and rodent lineages to shed light on the structure and evolution of genomes and genes. Notably, the majority of the most highly conserved non-coding sequences in mammalian genomes are clustered near a small subset of genes with important roles in development. Analysis of SNPs reveals long-range haplotypes across the entire dog genome, and defines the nature of genetic diversity within and across breeds. The current SNP map now makes it possible for genome-wide association studies to identify genes responsible for diseases and traits, with important consequences for human and companion animal health.
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- Arrillaga-Romany, Isabel, et al.
(author)
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Performance of a Hospital Pathway for Patients With a New Single Brain Mass
- 2019
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In: JOURNAL OF ONCOLOGY PRACTICE. - : American Society of Clinical Oncology (ASCO). - 1554-7477. ; 15:3, s. e211-e218
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Journal article (peer-reviewed)abstract
- WHAT WE FOUND:Length of stay and time to surgery were significantly reduced after implementation of this admission pathway. Readmission rate was not adversely affected by this change. The protocol also significantly reduced the number of unnecessary body computed tomography imaging studies obtained in this patient population.CONFOUNDING FACTORS/REAL-LIFE IMPLICATIONS:The results of this study should be interpreted with their retrospective nature in mind. Further, analysis of this admission pathway did not take into consideration patient perspective or cost implications. Finally, the authors recognize that the resources for such an operational shift may only be found in large, tertiary, referral centers.Optimized specialized care for patients with new single brain masses promotes improved health care outcomes. It may also predictively reduce health care costs and improve patient satisfaction. More research is needed in this field. Limitations to our study included the inherent limitations of a retrospective pre-post design that can make it difficult to separate the effect of a specific intervention from other factors that change over time. In addition, assessment of patient satisfaction, use of diagnostic tests beyond body imaging, and advanced cost analysis could have strengthened this study. Lastly, it should be noted that the applicability of our approach may be limited to major tertiary centers with enough resources to implement such a pathway.Purpose:To reduce care variation and improve the management of patients with newly identified single brain masses and no history of cancer, we implemented a dedicated admission protocol.Methods:We reviewed records of 206 patients who presented to our emergency department between January 2010 and May 2016 with a new single brain mass but no history of cancer. Patients admitted before the protocol implementation were designated the pre-implementation group (PRE), and those admitted after implementation were designated the post-implementation group (POST).Results:Ninety-six patients were in the PRE group and 110 in the POST group. Length of stay for POST patients was significantly shorter than for PRE patients (6 v 7 days, respectively; P = .042), and this effect was more robust after excluding the 66 patients who were discharged to rehabilitation, skilled nursing, or hospice facilities (5 v 7 days, respectively; P = .001). Additional comparison of POST with PRE patients showed that time to surgery was significantly reduced (2.7 v 3.5 days, respectively; P = .006) and that computed tomography scans of the chest, abdomen, and pelvis were reduced (12% v 47%, respectively; P < .001). No difference was found in the 30-day readmission rates. For patients with GBM, there also was no significant difference in time to initiation of chemoradiation or in median overall survival.Conclusion:Implementation of a specialized admission pathway for patients with a new single brain mass decreased average length of hospital stay and time to surgery and reduced unnecessary diagnostic imaging tests in patients with primary brain tumors.
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| 10. |
- Juratli, Tareq A., et al.
(author)
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Targeted treatment of papillary craniopharyngiomas harboring BRAF V600E mutations
- 2019
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In: Cancer. - : WILEY. - 0008-543X .- 1097-0142. ; 125:17, s. 2910-2914
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Journal article (other academic/artistic)abstract
- Papillary craniopharyngiomas (PCPs) are characterized by the presence of BRAF V600E mutations, which are emerging as a useful guide for diagnosis and treatment decision making. The ongoing multicenter phase 2 Alliance A071601 trial is evaluating the efficacy of BRAF and mitogen-activated protein kinase kinase (MEK) inhibitors for patients with PCPs. With continued successful responses, it is proposed that BRAF (and MEK) inhibitors be evaluated for the neoadjuvant treatment of patients with PCPs.
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| 11. |
- Yang, Kexin, et al.
(author)
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Magneto-optic response of the metallic antiferromagnet Fe2As to ultrafast temperature excursions
- 2019
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In: Physical Review Materials. - : AMER PHYSICAL SOC. - 2475-9953. ; 3:12
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Journal article (peer-reviewed)abstract
- The linear magneto-optic Kerr effect (MOKE) is often used to probe magnetism of ferromagnetic materials, but MOKE cannot be applied to collinear antiferromagnets due to the cancellation of sublattice magnetization. Magneto-optic constants that are quadratic in magnetization, however, provide an approach for studying antiferromagnets on picosecond timescales. Here, we combine transient measurements of linear birefringence and optical reflectivity to study the optical response of Fe2As to small ultrafast temperature excursions. We performed temperature-dependent pump-probe measurements on crystallographically isotropic (001) and anisotropic (010) faces of Fe2As bulk crystals. We find that the largest optical signals arise from changes in the index of refraction along the z axis, perpendicular to the Ned vector. Both real and imaginary parts of the transient optical birefringence signal approximately follow the temperature dependence of the magnetic heat capacity, as expected if the changes in dielectric function are dominated by contributions of exchange interactions to the dielectric function.
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| 12. |
- Yang, Kexin, et al.
(author)
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Magnetocrystalline anisotropy of the easy-plane metallic antiferromagnet Fe2As
- 2020
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In: Physical Review B. - 2469-9950 .- 2469-9969. ; 102:6
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Journal article (peer-reviewed)abstract
- Magnetocrystalline anisotropy is a fundamental property of magnetic materials that determines the dynamics of magnetic precession, the frequency of spin waves, the thermal stability of magnetic domains, and the efficiency of spintronic devices. We combine torque magnetometry and density functional theory calculations to determine the magnetocrystalline anisotropy of the metallic antiferromagnet Fe2As. Fe2As has a tetragonal crystal structure with the Neel vector lying in the (001) plane. We report that the fourfold magnetocrystalline anisotropy in the (001) plane of Fe2As is extremely small, K-22 = -150 J/m(3) at T = 4 K, much smaller than the perpendicular magnetic anisotropy of ferromagnetic structure widely used in spintronic devices. K-22 is strongly temperature dependent and close to zero at T > 150 K. The anisotropy K-1 in the (010) plane is too large to be measured by torque magnetometry and we determine K-1 = -830 kJ/m(3) using first-principles density functional theory. Our simulations show that the contribution to the anisotropy from classical magnetic dipole-dipole interactions is comparable to the contribution from spin-orbit coupling. The calculated fourfold anisotropy in the (001) plane K-22 ranges from -290 to 280 J/m(3), the same order of magnitude as the measured value. We used K-1 from theory to predict the frequency and polarization of the lowest frequency antiferromagnetic resonance mode and find that the mode is linearly polarized in the (001) plane with f = 670 GHz.
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| 13. |
- Zheng, Qiye, et al.
(author)
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Thermal transport through the magnetic martensitic transition in MnxMGe(M = Co, Ni)
- 2018
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In: Physical Review Materials. - College Park : American Physical Society. - 2475-9953. ; 2:7
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Journal article (peer-reviewed)abstract
- We report on changes in the thermal conductivity of solid-state synthesized MnxMGe (M = Co, Ni, 0.98 < x < 1.02) alloys through their temperature-induced martensitic structural transition. The thermal conductivity is measured by time-domain thermoreflectance. Mn1.014NiGe exhibits an increase in thermal conductivity from 11 to 15.5 W m(-1) K-1 from approximately 575 to 625 K, and Mn1.007CoGe exhibits an increase in thermal conductivity from 7 to 8.5 W m(-1) K-1 from 500 to 550 K. In MnxNiGe, the transition temperature and the magnitude of the change in thermal conductivity are strongly dependent on the alloy composition. Our study advances the fundamental understanding of the thermal transport properties in the MnxMGe(M = Co, Ni) family of alloys and opens a new direction in the search for solid-state phase transition materials with potential applications as thermal regulators.
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