| 1. |
- Ferrario, M., et al.
(författare)
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IRIDE : Interdisciplinary research infrastructure based on dual electron linacs and lasers
- 2014
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Ingår i: Nuclear Instruments and Methods in Physics Research Section A. - : Elsevier BV. - 0168-9002 .- 1872-9576. ; 740, s. 138-146
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Tidskriftsartikel (refereegranskat)abstract
- This paper describes the scientific aims and potentials as well as the preliminary technical design of RUDE, an innovative tool for multi-disciplinary investigations in a wide field of scientific, technological and industrial applications. IRIDE will be a high intensity "particles factory", based on a combination of high duty cycle radio-frequency superconducting electron linacs and of high energy lasers. Conceived to provide unique research possibilities for particle physics, for condensed matter physics, chemistry and material science, for structural biology and industrial applications, IRIDE will open completely new research possibilities and advance our knowledge in many branches of science and technology. [RIDE is also supposed to be realized in subsequent stages of development depending on the assigned priorities.
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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. |
- Oikonomou, Vasileios, et al.
(författare)
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The Role of Interferon-γ in Autoimmune Polyendocrine Syndrome Type 1.
- 2024
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Ingår i: The New England journal of medicine. - 1533-4406. ; 390:20, s. 1873-1884
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Tidskriftsartikel (refereegranskat)abstract
- Autoimmune polyendocrine syndrome type 1 (APS-1) is a life-threatening, autosomal recessive syndrome caused by autoimmune regulator (AIRE) deficiency. In APS-1, self-reactive T cells escape thymic negative selection, infiltrate organs, and drive autoimmune injury. The effector mechanisms governing T-cell-mediated damage in APS-1 remain poorly understood.We examined whether APS-1 could be classified as a disease mediated by interferon-γ. We first assessed patients with APS-1 who were participating in a prospective natural history study and evaluated mRNA and protein expression in blood and tissues. We then examined the pathogenic role of interferon-γ using Aire-/-Ifng-/- mice and Aire-/- mice treated with the Janus kinase (JAK) inhibitor ruxolitinib. On the basis of our findings, we used ruxolitinib to treat five patients with APS-1 and assessed clinical, immunologic, histologic, transcriptional, and autoantibody responses.Patients with APS-1 had enhanced interferon-γ responses in blood and in all examined autoimmunity-affected tissues. Aire-/- mice had selectively increased interferon-γ production by T cells and enhanced interferon-γ, phosphorylated signal transducer and activator of transcription 1 (pSTAT1), and CXCL9 signals in multiple organs. Ifng ablation or ruxolitinib-induced JAK-STAT blockade in Aire-/- mice normalized interferon-γ responses and averted T-cell infiltration and damage in organs. Ruxolitinib treatment of five patients with APS-1 led to decreased levels of T-cell-derived interferon-γ, normalized interferon-γ and CXCL9 levels, and remission of alopecia, oral candidiasis, nail dystrophy, gastritis, enteritis, arthritis, Sjögren's-like syndrome, urticaria, and thyroiditis. No serious adverse effects from ruxolitinib were identified in these patients.Our findings indicate that APS-1, which is caused by AIRE deficiency, is characterized by excessive, multiorgan interferon-γ-mediated responses. JAK inhibition with ruxolitinib in five patients showed promising results. (Funded by the National Institute of Allergy and Infectious Diseases and others.).
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| 4. |
- Kreins, AY, et al.
(författare)
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Human TYK2 deficiency: Mycobacterial and viral infections without hyper-IgE syndrome
- 2015
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Ingår i: The Journal of experimental medicine. - : Rockefeller University Press. - 1540-9538 .- 0022-1007. ; 212:10, s. 1641-1662
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Tidskriftsartikel (refereegranskat)abstract
- Autosomal recessive, complete TYK2 deficiency was previously described in a patient (P1) with intracellular bacterial and viral infections and features of hyper-IgE syndrome (HIES), including atopic dermatitis, high serum IgE levels, and staphylococcal abscesses. We identified seven other TYK2-deficient patients from five families and four different ethnic groups. These patients were homozygous for one of five null mutations, different from that seen in P1. They displayed mycobacterial and/or viral infections, but no HIES. All eight TYK2-deficient patients displayed impaired but not abolished cellular responses to (a) IL-12 and IFN-α/β, accounting for mycobacterial and viral infections, respectively; (b) IL-23, with normal proportions of circulating IL-17+ T cells, accounting for their apparent lack of mucocutaneous candidiasis; and (c) IL-10, with no overt clinical consequences, including a lack of inflammatory bowel disease. Cellular responses to IL-21, IL-27, IFN-γ, IL-28/29 (IFN-λ), and leukemia inhibitory factor (LIF) were normal. The leukocytes and fibroblasts of all seven newly identified TYK2-deficient patients, unlike those of P1, responded normally to IL-6, possibly accounting for the lack of HIES in these patients. The expression of exogenous wild-type TYK2 or the silencing of endogenous TYK2 did not rescue IL-6 hyporesponsiveness, suggesting that this phenotype was not a consequence of the TYK2 genotype. The core clinical phenotype of TYK2 deficiency is mycobacterial and/or viral infections, caused by impaired responses to IL-12 and IFN-α/β. Moreover, impaired IL-6 responses and HIES do not appear to be intrinsic features of TYK2 deficiency in humans.
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| 5. |
- Toreti, A, et al.
(författare)
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Narrowing uncertainties in the effects of elevated CO2 on crops
- 2020
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Ingår i: Nature Food. - : Springer Science and Business Media LLC. - 2662-1355. ; 1, s. 775-782
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Tidskriftsartikel (refereegranskat)abstract
- Plant responses to rising atmospheric carbon dioxide (CO2) concentrations, together with projected variations in temperature and precipitation will determine future agricultural production. Estimates of the impacts of climate change on agriculture provide essential information to design effective adaptation strategies, and develop sustainable food systems. Here, we review the current experimental evidence and crop models on the effects of elevated CO2 concentrations. Recent concerted efforts have narrowed the uncertainties in CO2-induced crop responses so that climate change impact simulations omitting CO2 can now be eliminated. To address remaining knowledge gaps and uncertainties in estimating the effects of elevated CO2 and climate change on crops, future research should expand experiments on more crop species under a wider range of growing conditions, improve the representation of responses to climate extremes in crop models, and simulate additional crop physiological processes related to nutritional quality.
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| 6. |
- Aprojanz, J., et al.
(författare)
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High-Mobility Epitaxial Graphene on Ge/Si(100) Substrates
- 2020
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Ingår i: ACS applied materials & interfaces. - : American Chemical Society (ACS). - 1944-8244 .- 1944-8252. ; 12:38, s. 43065-43072
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Tidskriftsartikel (refereegranskat)abstract
- Graphene was shown to reveal intriguing properties of its relativistic two-dimensional electron gas; however, its implementation to microelectronic applications is missing to date. In this work, we present a comprehensive study of epitaxial graphene on technologically relevant and in a standard CMOS process achievable Ge(100) epilayers grown on Si(100) substrates. Crystalline graphene monolayer structures were grown by means of chemical vapor deposition (CVD). Using angle-resolved photoemission spectroscopy and in situ surface transport measurements, we demonstrate their metallic character both in momentum and real space. Despite numerous crystalline imperfections, e.g., grain boundaries and strong corrugation, as compared to epitaxial graphene on SiC(0001), charge carrier mobilities of 1 × 104 cm2/Vs were obtained at room temperature, which is a result of the quasi-charge neutrality within the graphene monolayers on germanium and not dependent on the presence of an interface oxide. The interface roughness due to the facet structure of the Ge(100) epilayer, formed during the CVD growth of graphene, can be reduced via subsequent in situ annealing up to 850 °C coming along with an increase in the mobility by 30%. The formation of a Ge(100)-(2 × 1) structure demonstrates the weak interaction and effective delamination of graphene from the Ge/Si(100) substrate.
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| 7. |
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| 8. |
- Sharma, Ram A, et al.
(författare)
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Obstructive Sleep Apnea Severity Affects Amyloid Burden in Cognitively Normal Elderly: A Longitudinal Study.
- 2018
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Ingår i: American Journal of Respiratory and Critical Care Medicine. - 1073-449X .- 1535-4970. ; 197:7, s. 933-943
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Tidskriftsartikel (refereegranskat)abstract
- Recent evidence suggests that Obstructive Sleep Apnea (OSA) may be a risk factor for developing Mild Cognitive Impairment and Alzheimer's disease. However, how sleep apnea affects longitudinal risk for Alzheimer's disease is less well understood.To test the hypothesis that there is an association between severity of OSA and longitudinal increase in amyloid burden in cognitively normal elderly.Data was derived from a 2-year prospective longitudinal study that sampled community-dwelling healthy cognitively normal elderly. Subjects were healthy volunteers between the ages of 55 to 90, were non-depressed and had a consensus clinical diagnosis of cognitively normal. CSF Amyloid beta was measured using ELISA. Subjects received Pittsburgh compound B Positron Emission Tomography scans following standardized procedures. Monitoring of OSA was completed using a home sleep recording device.We found that severity of OSA indices (lnAHIall [F1,88=4.26, p<.05] and lnAHI4% [F1,87=4.36, p<.05]) were associated with annual rate of change of CSF Aβ42 using linear regression after adjusting for age, sex, BMI and ApoE4 status. LnAHIall and lnAHI4 were not associated with increases in ADPiB-mask most likely due to the small sample size although there was a trend for lnAHIall (F1,28=2.96, p=.09 and F1,28=2.32, n.s. respectively).In a sample of cognitively normal elderly, OSA was associated with markers of increased amyloid burden over the 2 year follow-up. Sleep fragmentation and/or intermittent hypoxia from OSA are likely candidate mechanisms. If confirmed, clinical interventions for OSA may be useful in preventing amyloid build-up in cognitively normal elderly.
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| 9. |
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| 10. |
- Chang, Heejun, et al.
(författare)
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Assessment of urban flood vulnerability using the social-ecological-technological systems framework in six US cities
- 2021
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Ingår i: Sustainable cities and society. - : Elsevier BV. - 2210-6707. ; 68
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Tidskriftsartikel (refereegranskat)abstract
- As urban populations continue to grow through the 21st century, more people are projected to be at risk of exposure to climate change-induced extreme events. To investigate the complexity of urban floods, this study applied an interlinked social-ecological-technological systems (SETS) vulnerability framework by developing an urban flood vulnerability index for six US cities. Indicators were selected to reflect and illustrate exposure, sensitivity, and adaptive capacity to flooding for each of the three domains of SETS. We quantified 18 indicators and normalized them by the cities' 500-yr floodplain area at the census block group level. Clusters of flood vulnerable areas were identified differently by each SETS domain, and some areas were vulnerable to floods in more than one domain. Results are provided to support decision-making for reducing risks to flooding, by considering social, ecological, and technological vulnerability as well as hotspots where multiple sources of vulnerability coexist. The spatially explicit urban SETS flood vulnerability framework can be transferred to other regions facing challenging urban floods and other types of environmental hazards. Mapping SETS flood vulnerability helps to reveal intersections of complex SETS interactions and inform policy-making for building more resilient cities in the face of extreme events and climate change impacts.
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| 11. |
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| 12. |
- Deryng, Delphine, et al.
(författare)
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Regional disparities in the beneficial effects of rising CO2 concentrations on crop water productivity
- 2016
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Ingår i: Nature Climate Change. - : Springer Science and Business Media LLC. - 1758-678X .- 1758-6798. ; 6:8, s. 786-790
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Tidskriftsartikel (refereegranskat)abstract
- Rising atmospheric CO2 concentrations ([CO2 ]) are expected to enhance photosynthesis and reduce crop water use. However, there is high uncertainty about the global implications of these effects for future crop production and agricultural water requirements under climate change. Here we combine results from networks of field experiments and global crop models to present a spatially explicit global perspective on crop water productivity (CWP, the ratio of crop yield to evapotranspiration) for wheat, maize, rice and soybean under elevated [CO2 ] and associated climate change projected for a high-end greenhouse gas emissions scenario. We find CO2 effects increase global CWP by 10[0;47]%-27[7;37]% (median[interquartile range] across the model ensemble) by the 2080s depending on crop types, with particularly large increases in arid regions (by up to 48[25;56]% for rainfed wheat). If realized in the fields, the effects of elevated [CO2 ] could considerably mitigate global yield losses whilst reducing agricultural consumptive water use (4-17%). We identify regional disparities driven by differences in growing conditions across agro-ecosystems that could have implications for increasing food production without compromising water security. Finally, our results demonstrate the need to expand field experiments and encourage greater consistency in modelling the effects of rising [CO2 ] across crop and hydrological modelling communities.
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| 13. |
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| 14. |
- Karakachian, Hrag, et al.
(författare)
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One-dimensional confinement and width-dependent bandgap formation in epitaxial graphene nanoribbons
- 2020
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Ingår i: Nature Communications. - : NATURE RESEARCH. - 2041-1723. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- The ability to define an off state in logic electronics is the key ingredient that is impossible to fulfill using a conventional pristine graphene layer, due to the absence of an electronic bandgap. For years, this property has been the missing element for incorporating graphene into next-generation field effect transistors. In this work, we grow high-quality armchair graphene nanoribbons on the sidewalls of 6H-SiC mesa structures. Angle-resolved photoelectron spectroscopy (ARPES) and scanning tunneling spectroscopy measurements reveal the development of a width-dependent semiconducting gap driven by quantum confinement effects. Furthermore, ARPES demonstrates an ideal one-dimensional electronic behavior that is realized in a graphene-based environment, consisting of well-resolved subbands, dispersing and non-dispersing along and across the ribbons respectively. Our experimental findings, coupled with theoretical tight-binding calculations, set the grounds for a deeper exploration of quantum confinement phenomena and may open intriguing avenues for new low-power electronics. Here, the authors investigate armchair graphene nanoribbons by angle-resolved photoelectron spectroscopy, and show the development of a width-dependent semiconducting gap driven by quantum confinement effects, and an ideal one-dimensional electronic behaviour.
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| 15. |
- Karakachian, Hrag, et al.
(författare)
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Periodic Nanoarray of Graphene pn-Junctions on Silicon Carbide Obtained by Hydrogen Intercalation
- 2022
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Ingår i: Advanced Functional Materials. - : Wiley-V C H Verlag GMBH. - 1616-301X .- 1616-3028. ; 32:18
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Tidskriftsartikel (refereegranskat)abstract
- Graphene pn-junctions offer a rich portfolio of intriguing physical phenomena. They stand as the potential building blocks for a broad spectrum of future technologies, ranging from electronic lenses analogous to metamaterials in optics, to high-performance photodetectors important for a variety of optoelectronic applications. The production of graphene pn-junctions and their precise structuring at the nanoscale remains to be a challenge. In this work, a scalable method for fabricating periodic nanoarrays of graphene pn-junctions on a technologically viable semiconducting SiC substrate is introduced. Via H-intercalation, 1D confined armchair graphene nanoribbons are transformed into a single 2D graphene sheet rolling over 6H-SiC mesa structures. Due to the different surface terminations of the basal and vicinal SiC planes constituting the mesa structures, different types of charge carriers are locally induced into the graphene layer. Using angle-resolved photoelectron spectroscopy, the electronic band structure of the two graphene regions are selectively measured, finding two symmetrically doped phases with p-type being located on the basal planes and n-type on the facets. The results demonstrate that through a careful structuring of the substrate, combined with H-intercalation, integrated networks of graphene pn-junctions could be engineered at the nanoscale, paving the way for the realization of novel optoelectronic device concepts.
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| 16. |
- Kuusk, Teele, et al.
(författare)
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Topographic distribution of first landing sites of lymphatic metastases from patients with renal cancer
- 2020
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Ingår i: Urologic Oncology. - : Elsevier. - 1078-1439 .- 1873-2496. ; 38:5, s. 521-525
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Tidskriftsartikel (refereegranskat)abstract
- INTRODUCTION AND OBJECTIVE: Adjuvant studies with checkpoint inhibitors have attracted new interest in accurate pathological lymph node (LN) staging in renal cell carcinoma. Sentinel lymph node (SN) studies in cN0 patients revealed the pattern of lymphatic radiotracer drainage from renal tumors. The aim of this study was to describe the location of single- or oligometastatic LN and analyze if the topography of these first landing sites matches the drainage pattern observed in SN studies of renal tumors.MATERIALS AND METHODS: We collected data from 8 referral centers from 1990 to 2018 of all patients with pT1-4 cN0 or cN1 M0 renal cell carcinoma with pathologically confirmed single- or oligometastases in locoregional LN. The location of LN metastases, number, size of metastatic LN, and survival were analyzed using descriptive statistics with SPSS version 22 (IBM, Chicago, IL).RESULTS: From 3,794 patients with histologically confirmed pN1, a total of 76 patients (2%) with single- or oligometastatic pN1 were identified, of whom 24 (31.6%) and 52 (68.4%) were cN0 and cN1, respectively. On the left side, LN metastases were predominantly located in the para-aortal (48.0%; 95% confidence interval [CI] 29.22-63.12%) and hilar (31.42%; 95% CI 17.4-49.4%) area. On the right side, metastases located in retrocaval (26.82%; 95% CI 14.7-43.2%), hilar (26.82%; 95% CI 14.7-43.2%), interaortocaval (26.82%; 95% CI 14.7-43.2%), and paracaval (17.07%; 95% CI 7.6-32.6%) LNs. These landing sites exactly matched the lymphatic drainage pattern of intratumorally injected radiotracer reported in SN studies for both sides.CONCLUSIONS: Single- or oligometastatic LNs in renal cancer are mainly located in the hilar, retro-, para, and interaortocaval region on the right side and para-aortal region on the left side. These first landing sites match the drainage pattern reported in SN trials.
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| 17. |
- Müller, Christoph, et al.
(författare)
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The Global Gridded Crop Model Intercomparison phase 1 simulation dataset
- 2019
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Ingår i: Scientific Data. - : Springer Science and Business Media LLC. - 2052-4463. ; 6:1
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Tidskriftsartikel (refereegranskat)abstract
- The Global Gridded Crop Model Intercomparison (GGCMI) phase 1 dataset of the Agricultural Model Intercomparison and Improvement Project (AgMIP) provides an unprecedentedly large dataset of crop model simulations covering the global ice-free land surface. The dataset consists of annual data fields at a spatial resolution of 0.5 arc-degree longitude and latitude. Fourteen crop modeling groups provided output for up to 11 historical input datasets spanning 1901 to 2012, and for up to three different management harmonization levels. Each group submitted data for up to 15 different crops and for up to 14 output variables. All simulations were conducted for purely rainfed and near-perfectly irrigated conditions on all land areas irrespective of whether the crop or irrigation system is currently used there. With the publication of the GGCMI phase 1 dataset we aim to promote further analyses and understanding of crop model performance, potential relationships between productivity and environmental impacts, and insights on how to further improve global gridded crop model frameworks. We describe dataset characteristics and individual model setup narratives.
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| 18. |
- Neely, G Gregory, et al.
(författare)
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A Genome-wide Drosophila Screen for Heat Nociception Identifies alpha 2 delta 3 as an Evolutionarily Conserved Pain Gene
- 2010
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Ingår i: Cell. - : Elsevier Science B.V., Amsterdam.. - 0092-8674 .- 1097-4172. ; 143:4, s. 628-638
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Tidskriftsartikel (refereegranskat)abstract
- Worldwide, acute, and chronic pain affects 20% of the adult population and represents an enormous financial and emotional burden. Using genome-wide neuronal-specific RNAi knockdown in Drosophila, we report a global screen for an innate behavior and identify hundreds of genes implicated in heat nociception, including the alpha 2 delta family calcium channel subunit straightjacket (stj). Mice mutant for the stj ortholog CACNA2D3 (alpha 2 delta 3) also exhibit impaired behavioral heat pain sensitivity. In addition, in humans, alpha 2 delta 3 SNP variants associate with reduced sensitivity to acute noxious heat and chronic back pain. Functional imaging in alpha 2 delta 3 mutant mice revealed impaired transmission of thermal pain-evoked signals from the thalamus to higher-order pain centers. Intriguingly, in alpha 2 delta 3 mutant mice, thermal pain and tactile stimulation triggered strong cross-activation, or synesthesia, of brain regions involved in vision, olfaction, and hearing.
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| 19. |
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| 20. |
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| 21. |
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| 22. |
- Ruane, Alex C., et al.
(författare)
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Strong regional influence of climatic forcing datasets on global crop model ensembles
- 2021
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Ingår i: Agricultural and Forest Meteorology. - : Elsevier BV. - 0168-1923. ; 300
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Tidskriftsartikel (refereegranskat)abstract
- We present results from the Agricultural Model Intercomparison and Improvement Project (AgMIP) Global Gridded Crop Model Intercomparison (GGCMI) Phase I, which aligned 14 global gridded crop models (GGCMs) and 11 climatic forcing datasets (CFDs) in order to understand how the selection of climate data affects simulated historical crop productivity of maize, wheat, rice and soybean. Results show that CFDs demonstrate mean biases and differences in the probability of extreme events, with larger uncertainty around extreme precipitation and in regions where observational data for climate and crop systems are scarce. Countries where simulations correlate highly with reported FAO national production anomalies tend to have high correlations across most CFDs, whose influence we isolate using multi-GGCM ensembles for each CFD. Correlations compare favorably with the climate signal detected in other studies, although production in many countries is not primarily climate-limited (particularly for rice). Bias-adjusted CFDs most often were among the highest model-observation correlations, although all CFDs produced the highest correlation in at least one top-producing country. Analysis of larger multi-CFD-multi-GGCM ensembles (up to 91 members) shows benefits over the use of smaller subset of models in some regions and farming systems, although bigger is not always better. Our analysis suggests that global assessments should prioritize ensembles based on multiple crop models over multiple CFDs as long as a top-performing CFD is utilized for the focus region.
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| 23. |
- Stanford, K, et al.
(författare)
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Exercise Metabolism
- 2017
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Ingår i: Cell metabolism. - : Elsevier BV. - 1932-7420 .- 1550-4131. ; 25:5, s. 978-984
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Tidskriftsartikel (refereegranskat)
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