| 1. |
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- 2019
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Tidskriftsartikel (refereegranskat)
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| 2. |
- Bernal, Ximena E., et al.
(författare)
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Empowering Latina scientists
- 2019
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 363:6429, s. 825-826
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 3. |
- Grüning, Björn, et al.
(författare)
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Bioconda: A sustainable and comprehensive software distribution for the life sciences
- 2017
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- We present Bioconda (https://bioconda.github.io), a distribution of bioinformatics software for the lightweight, multi-platform and language-agnostic package manager Conda. Currently, Bioconda offers a collection of over 3000 software packages, which is continuously maintained, updated, and extended by a growing global community of more than 200 contributors. Bioconda improves analysis reproducibility by allowing users to define isolated environments with defined software versions, all of which are easily installed and managed without administrative privileges.
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| 4. |
- Schwager, Evelyn E., et al.
(författare)
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The house spider genome reveals an ancient whole-genome duplication during arachnid evolution
- 2017
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Ingår i: BMC Biology. - : BIOMED CENTRAL LTD. - 1741-7007. ; 15
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Tidskriftsartikel (refereegranskat)abstract
- Background: The duplication of genes can occur through various mechanisms and is thought to make a major contribution to the evolutionary diversification of organisms. There is increasing evidence for a large-scale duplication of genes in some chelicerate lineages including two rounds of whole genome duplication (WGD) in horseshoe crabs. To investigate this further, we sequenced and analyzed the genome of the common house spider Parasteatoda tepidariorum.Results: We found pervasive duplication of both coding and non-coding genes in this spider, including two clusters of Hox genes. Analysis of synteny conservation across the P. tepidariorum genome suggests that there has been an ancient WGD in spiders. Comparison with the genomes of other chelicerates, including that of the newly sequenced bark scorpion Centruroides sculpturatus, suggests that this event occurred in the common ancestor of spiders and scorpions, and is probably independent of the WGDs in horseshoe crabs. Furthermore, characterization of the sequence and expression of the Hox paralogs in P. tepidariorum suggests that many have been subject to neo-functionalization and/or sub-functionalization since their duplication.Conclusions: Our results reveal that spiders and scorpions are likely the descendants of a polyploid ancestor that lived more than 450 MYA. Given the extensive morphological diversity and ecological adaptations found among these animals, rivaling those of vertebrates, our study of the ancient WGD event in Arachnopulmonata provides a new comparative platform to explore common and divergent evolutionary outcomes of polyploidization events across eukaryotes.
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| 5. |
- Abascal, Angela, et al.
(författare)
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Making Urban Slum Population Visible : Citizens and Satellites to Reinforce Slum Censuses
- 2024
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Ingår i: Urban Inequalities from Space. - : Springer. - 9783031491856 - 9783031491832 ; , s. 287-302
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Bokkapitel (refereegranskat)abstract
- In response to the “Leave No One Behind” principle (the central promise of the 2030 Agenda for Sustainable Development), reliable estimate of the total number of citizens living in slums is urgently needed but not available for some of the most vulnerable communities. Not having a reliable estimate of the number of poor urban dwellers limits evidence-based decision-making for proper resource allocation in the fight against urban inequalities. From a geographical perspective, urban population distribution maps in many low- and middle-income cities are most often derived from outdated or unreliable census data disaggregated by coarse administrative units. Moreover, slum populations are presented as aggregated within bigger administrative areas, leading to a large diffuse in the estimates. Existing global and open population databases provide homogeneously disaggregated information (i.e. in a spatial grid), but they mostly rely on census data to generate their estimates, so they do not provide additional information on the slum population. While a few studies have focused on bottom-up geospatial models for slum population mapping using survey data, geospatial covariates, and earth observation imagery, there is still a significant gap in methodological approaches for producing precise estimates within slums. To address this issue, we designed a pilot experiment to explore new avenues. We conducted this study in the slums of Nairobi, where we collected in situ data together with slum dwellers using a novel data collection protocol. Our results show that the combination of satellite imagery with in situ data collected by citizen science paves the way for generalisable, gridded estimates of slum populations. Furthermore, we find that the urban physiognomy of slums and population distribution patterns are related, which allows for highlighting the diversity of such patterns using earth observation within and between slums of the same city.
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| 6. |
- Adalsteinsson, Sigurbjörn Már, et al.
(författare)
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Correlating chemical composition and optical properties of photochromic rare-earth oxyhydrides using ion beam analysis
- 2020
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Ingår i: Nuclear Instruments and Methods in Physics Research Section B. - : ELSEVIER. - 0168-583X .- 1872-9584. ; 485, s. 36-40
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Tidskriftsartikel (refereegranskat)abstract
- We relate the photochromic response of rare-earth oxyhydride thin films (YHO, NdHO, GdHO and DyHO) synthesized by reactive magnetron sputtering to chemical composition. Depth profiles of the sample composition are extracted by a multi-method ion beam analysis approach. The total areal density of the thin films is deduced from Rutherford Backscattering Spectrometry while coincidence Time-of-Flight/Energy Elastic Recoil Detection Analysis provides depth-profiles of the film constituents. High-resolution depth profiles of the concentration of light species, i.e. hydrogen and oxygen, are additionally extracted from Nuclear Reaction Analysis and Elastic Backscattering Spectrometry, respectively. The photochromic response of the films is measured by optical transmission spectroscopy before and after illumination. We report photochromic properties for YHO, NdHO, GdHO and DyHO for chemical compositions described by the formula REH2-delta O delta in the range of 0.45 < 6 < 1.5.
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| 7. |
- Aranda-Guillén, Maribel, et al.
(författare)
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A polygenic risk score to help discriminate primary adrenal insufficiency of different etiologies.
- 2023
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Ingår i: Journal of internal medicine. - : John Wiley & Sons. - 0954-6820 .- 1365-2796. ; 294:1, s. 96-109
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Tidskriftsartikel (refereegranskat)abstract
- Autoimmune Addison's disease (AAD) is the most common cause of primary adrenal insufficiency (PAI). Despite its exceptionally high heritability, tools to estimate disease susceptibility in individual patients are lacking. We hypothesized that polygenic risk score (PRS) for AAD could help investigate PAI pathogenesis in pediatric patients.We here constructed and evaluated a PRS for AAD in 1223 seropositive cases and 4097 controls. To test its clinical utility, we reevaluated 18 pediatric patients, whose whole genome we also sequenced. We next explored the individual PRS in more than 120 seronegative patients with idiopathic PAI.The genetic susceptibility to AAD-quantified using PRS-was on average 1.5 standard deviations (SD) higher in patients compared with healthy controls (p<2e-16), and 1.2 SD higher in the young patients compared with the old (p=3e-4). Using the novel PRS, we searched for pediatric patients with strikingly low AAD susceptibility and identified cases of monogenic PAI, previously misdiagnosed as AAD. By stratifying seronegative adult patients by autoimmune comorbidities and disease duration we could delineate subgroups of PRS suggesting various disease etiologies.The PRS performed well for case-control differentiation and susceptibility estimation in individual patients. Remarkably, a PRS for AAD holds promise as a means to detect disease etiologies other than autoimmunity.
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| 8. |
- Artaza, Haydee, et al.
(författare)
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Rare copy number variation in autoimmune Addison's disease
- 2024
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Ingår i: Frontiers in Immunology. - : Frontiers Media S.A.. - 1664-3224. ; 15
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Tidskriftsartikel (refereegranskat)abstract
- Autoimmune Addison's disease (AAD) is a rare but life-threatening endocrine disorder caused by an autoimmune destruction of the adrenal cortex. A previous genome-wide association study (GWAS) has shown that common variants near immune-related genes, which mostly encode proteins participating in the immune response, affect the risk of developing this condition. However, little is known about the contribution of copy number variations (CNVs) to AAD susceptibility. We used the genome-wide genotyping data from Norwegian and Swedish individuals (1,182 cases and 3,810 controls) to investigate the putative role of CNVs in the AAD aetiology. Although the frequency of rare CNVs was similar between cases and controls, we observed that larger deletions (>1,000 kb) were more common among patients (OR = 4.23, 95% CI 1.85-9.66, p = 0.0002). Despite this, none of the large case-deletions were conclusively pathogenic, and the clinical presentation and an AAD-polygenic risk score were similar between cases with and without the large CNVs. Among deletions exclusive to individuals with AAD, we highlight two ultra-rare deletions in the genes LRBA and BCL2L11, which we speculate might have contributed to the polygenic risk in these carriers. In conclusion, rare CNVs do not appear to be a major cause of AAD but further studies are needed to ascertain the potential contribution of rare deletions to the polygenic load of AAD susceptibility.
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| 9. |
- Baba, Elbruz Murat, et al.
(författare)
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Preferential Orientation of Photochromic Gadolinium Oxyhydride Films
- 2020
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Ingår i: Molecules. - : MDPI. - 1431-5157 .- 1420-3049. ; 25:14
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Tidskriftsartikel (refereegranskat)abstract
- We report preferential orientation control in photochromic gadolinium oxyhydride (GdHO) thin films deposited by a two-step process. Gadolinium hydride (GdH2-x) films were grown by reactive magnetron sputtering, followed by oxidation in air. The preferential orientation, grain size, anion concentrations and photochromic response of the films were strongly dependent on the deposition pressure. The GdHO films showed a preferential orientation along the [100] direction and exhibited photochromism when synthesized at deposition pressures of up to 5.8 Pa. The photochromic contrast was larger than 20% when the films were deposited below 2.8 Pa with a 0.22 H-2/Ar flow ratio. We argue that the relation of preferential orientation and the post deposition oxidation since oxygen concentration is known to be a key parameter for photochromism in rare-earth oxyhydride thin films. The experimental observations described above were explained by the decrease of the grain size as a result of the increase of the deposition pressure of the sputtering gas, followed by a higher oxygen incorporation.
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| 10. |
- Barker, Philip A., et al.
(författare)
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Carbon cycling within an East African lake revealed by the carbon isotope composition of diatom silica: a 25-ka record from Lake Challa, Mt. Kilimanjaro
- 2013
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Ingår i: Quaternary Science Reviews. - : Elsevier BV. - 0277-3791. ; 66, s. 55-63
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Tidskriftsartikel (refereegranskat)abstract
- The carbon cycle of a lake is a balance between supply from the atmosphere and catchment, and the net demand exerted by primary producers, minus losses back to the atmosphere and to sediment storage. Evaluating the sum of these processes and reconstructing them from sediment records of lake history requires a range of methods and a multi-proxy approach. One promising technique is to explore the carbon-isotope composition (delta C-13(diatom)) of organic matter incorporated within the silica frustules of diatom algae. Here we present a 25,000-year record of delta C-13(diatom) from the sediments of crater Lake Challa on the eastern flank of Mt. Kilimanjaro, and along with other proxy data we make inferences about the three major phases in the history of the lake's carbon cycle. From 25 ka to 15.8 ka years BP, delta C-13(diatom) is positively correlated with the delta C-13 of bulk sediment organic matter (delta C-13(bulk)), indicating that high diatom productivity, as recorded by high % biogenic silica at this time, was preferentially removing C-12 and enriching the delta C-13 of lake-water dissolved inorganic carbon. From 15.8 to 5.5 ka the correlation between delta C-13(diatom) and delta C-13(bulk) breaks down, suggesting carbon supply to the lake satisfied or exceeded the demand from productivity. From 5.5 ka BP the positive correlation resumes, indicating an increase in the internal demand for carbon relative to external supply. Diatom frustule-bound carbon isotopes offer an original tool in examining long-term fluctuations in a lake's carbon budget and how the balance between supply and demand has changed through time. (C) 2012 Elsevier Ltd. All rights reserved.
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