| 1. |
- Göransson, Jenny, 1978-, et al.
(författare)
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A single molecule array for digital targeted molecular analyses
- 2009
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Ingår i: Nucleic Acids Research. - England : Oxford University Press. - 0305-1048 .- 1362-4962. ; 37:1, s. e7-
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Tidskriftsartikel (refereegranskat)abstract
- We present a new random array format together with a decoding scheme for targeted multiplex digital molecular analyses. DNA samples are analyzed using multiplex sets of padlock or selector probes that create circular DNA molecules upon target recognition. The circularized DNA molecules are amplified through rolling-circle amplification (RCA) to generate amplified single molecules (ASMs). A random array is generated by immobilizing all ASMs on a microscopy glass slide. The ASMs are identified and counted through serial hybridizations of small sets of tag probes, according to a combinatorial decoding scheme. We show that random array format permits at least 10 iterations of hybridization, imaging and dehybridization, a process required for the combinatorial decoding scheme. We further investigated the quantitative dynamic range and precision of the random array format. Finally, as a demonstration, the decoding scheme was applied for multiplex quantitative analysis of genomic loci in samples having verified copy-number variations. Of 31 analyzed loci, all but one were correctly identified and responded according to the known copy-number variations. The decoding strategy is generic in that the target can be any biomolecule which has been encoded into a DNA circle via a molecular probing reaction.
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| 2. |
- Lin, Yii Lih, 1978, et al.
(författare)
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Optical maps of plasmids as a proxy for clonal spread of MDR bacteria: A case study of an outbreak in a rural Ethiopian hospital
- 2020
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Ingår i: Journal of Antimicrobial Chemotherapy. - : Oxford University Press (OUP). - 0305-7453 .- 1460-2091. ; 75:10, s. 2804-2811
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Tidskriftsartikel (refereegranskat)abstract
- Objectives: MDR bacteria have become a prevailing health threat worldwide. We here aimed to use optical DNA mapping (ODM) as a rapid method to trace nosocomial spread of bacterial clones and gene elements.We believe that this method has the potential to be a tool of pivotal importance for MDR control. Methods: Twenty-four Escherichia coli samples of ST410 from three different wards were collected at an Ethiopian hospital and their plasmids were analysed by ODM. Plasmids were specifically digested with Cas9 targeting the antibiotic resistance genes, stained by competitive binding and confined in nanochannels for imaging. The resulting intensity profiles (barcodes) for each plasmid were compared to identify potential clonal spread of resistant bacteria. Results: ODM demonstrated that a large fraction of the patients carried bacteria with a plasmid of the same origin, carrying the ESBL gene blaCTX-M-15, suggesting clonal spread. The results correlate perfectly with core genome (cg)MLST data, where bacteria with the same plasmid also had very similar cgMLST profiles. Conclusions: ODM is a rapid discriminatory method for identifying plasmids and antibiotic resistance genes. Long-range deletions/insertions, which are challenging for short-read next-generation sequencing, can be easily identified and used to trace bacterial clonal spread. We propose that plasmid typing can be a useful tool to identify clonal spread of MDR bacteria. Furthermore, the simplicity of the method enables possible future application in low-and middle-income countries.
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| 3. |
- Fager, Christian, 1974, et al.
(författare)
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IC Design Aspects for 5G mm-Wave Systems
- 2020
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Ingår i: 2020 50TH EUROPEAN MICROWAVE CONFERENCE (EUMC). - 2325-0305. - 9782874870590 ; , s. 870-871
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)
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| 4. |
- Silva, G. A. R., et al.
(författare)
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Intra and interspecific sequence variation in closely related species of Cereus (CACTACEAE)
- 2016
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Ingår i: Biochemical Systematics and Ecology. - : Elsevier BV. - 0305-1978. ; 65, s. 137-142
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Tidskriftsartikel (refereegranskat)abstract
- In comparative phylogenetic and population genetic studies, one of the most crucial steps is to select appropriate DNA markers, a decision based primarily on the estimated variation in markers in cross-taxonomic surveys. To assess whether genetic variation at the intraspecific level in one species predicts the variation in another closely related species we used two congeneric species of Cereus (Cactaceae: Cereeae). We screened and characterized eight noncoding plastid regions (trnS-trnG, atpI-atpH, trnT-trnL, psbD-trnT, petL-psbE, 3'rps16-5'trnk, trnG intron, and trnL intron), and one nuclear gene (PhyC) in Cereus fernambucensis and C. hildmannianus. A total of 40 individuals from 15 populations were characterized according to nucleotide diversity, number of haplotypes, and number of potentially informative characters. The results revealed that nucleotide substitutions and indels are the main source of variation, with the largest divergence between species found in trnS-trnG. The trnL intron and petL-psbE showed intraspecific variability in both species. The psbD-trnT, atpI-atpH, trnS-trnG, and trnT-trnL, which are the most variable regions in one species, showed no variation in the other. Finally, the nuclear gene PhyC showed more resolution between Cereus species than within species. We thus found considerable heterogeneity among widely used plastid markers, even between closely related species, and suggest the use of PhyC as a marker for phylogenetic inference in these species. These results reinforce the need of screening as a preliminary step to conduct phylogeographic or phylogenetic studies in face of unpredictable sequence variation of molecular markers in plants. (C) 2016 Elsevier Ltd. All rights reserved.
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| 5. |
- Hultman, Lisa, 1978-, et al.
(författare)
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Employing Local Peacekeeping Data to Forecast Changes in Violence
- 2022
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Ingår i: International Interactions. - : Taylor & Francis Group. - 0305-0629 .- 1547-7444. ; 48:4, s. 823-840
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Tidskriftsartikel (refereegranskat)abstract
- One way of improving forecasts is through better data. We explore how much we can improve predictions of conflict violence by introducing data reflecting third-party efforts to manage violence. By leveraging new sub-national data on all UN peacekeeping deployments in Africa, 1994–2020, from the Geocoded Peacekeeping (Geo-PKO) dataset, we predict changes in violence at the local level. The advantage of data on peacekeeping deployments is that these vary over time and space, as opposed to many structural variables commonly used. We present two peacekeeping models that contain several local peacekeeping features, each with a separate set of additional variables that form the respective benchmark. The mean errors of our predictions only improve marginally. However, comparing observed and predicted changes in violence, the peacekeeping features improve our ability to identify the correct sign of the change. These results are particularly strong when we limit the sample to countries that have seen peacekeeping deployments. For an ambitious forecasting project, like ViEWS, it may thus be highly relevant to incorporate fine-grained and frequently updated data on peacekeeping troops.
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| 6. |
- Hultman, Lisa, 1978-
(författare)
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The Power to Hurt in Civil War : The Strategic Aim of Renamo Violence
- 2009
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Ingår i: Journal of Southern African Studies. - : Informa UK Limited. - 0305-7070 .- 1465-3893. ; 35:4, s. 821-834
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Tidskriftsartikel (refereegranskat)abstract
- This article develops a theoretical explanation for the seemingly indiscriminate violence used by Renamo during the civil war in Mozambique, a phenomenon which dominant theories on civil war violence cannot account for fully. The analysis builds on interviews with the Renamo leadership and Mozambican academics as well as secondary sources on the patterns of violence. It concludes that Renamo used mass violence to weaken the support for the government and create war fatigue. The main strategy was to cause enough damage to pressure the government into entering negotiations. The use of most violence against civilians in those areas where the population was believed to support the government, in combination with a clear objective to destabilise the government and a disciplined military organisation, support the argument that mass violence was employed to demonstrate ‘the power to hurt’.
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| 7. |
- Ilderton, Anton, 1978-, et al.
(författare)
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Symmetry breaking, conformal geometry and gauge invariance
- 2010
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Ingår i: Journal of Physics A. - : IOP Publishing. - 0305-4470 .- 1361-6447. ; 43:31, s. 312002-
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Tidskriftsartikel (refereegranskat)abstract
- When the electroweak action is rewritten in terms of SU(2) gauge-invariant variables, the Higgs can be interpreted as a conformal metric factor. We show that asymptotic flatness of the metric is required to avoid a Gribov problem: without it, the new variables fail to be nonperturbatively gauge invariant. We also clarify the relations between this approach and unitary gauge fixing, and the existence of similar transformations in other gauge theories.
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| 8. |
- Kainulainen, Kent, 1978-, et al.
(författare)
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Island hopping, long-distance dispersal and species radiation: historical biogeography of the Coffeeae alliance (Rubiaceae)
- 2017
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Ingår i: Journal of Biogeography. - : Wiley. - 0305-0270 .- 1365-2699. ; 44, s. 1966-1979
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Tidskriftsartikel (refereegranskat)abstract
- Aim. The Western Indian Ocean region (WIOR) is home to a very diverse and largely unique flora that has mainly originated via long-distance dispersals. The aim of this study is to gain insight into the origins of the WIOR biodiversity and to understand the dynamics of colonization events between the islands. We investigate spatial and temporal hypotheses of the routes of dispersal, and compare the dispersal patterns of plants of the Coffeeae alliance (Rubiaceae) and their dispersers. Rubiaceae is the second most species-rich plant family in Madagascar, and includes many endemic genera. The neighbouring archipelagos of the Comoros, Mascarenes and Seychelles also harbour several endemic Rubiaceae.Location. The islands of the Western Indian Ocean.Methods. Phylogenetic relationships and divergence times were reconstructed from plastid DNA data of an ingroup sample of 340 species, using Bayesian inference. Ancestral areas and range evolution history were inferred by a maximum likelihood method that takes topological uncertainty into account.Results. At least 15 arrivals to Madagascar were inferred, the majority of which have taken place within the last 10 Myr. Most dispersal events were supported as being from mainland Africa, but Catunaregam may have dispersed from Asia. Although most Coffeeae alliance lineages are zoochorous, the general pattern of dispersals from Africa is incongruent with the biogeographic origins of the extant Malagasy volant frugivores. Several out-of-Madagascar dispersals were inferred to the neighbouring islands, as well as back-colonizations of Africa.Main conclusions. The African flora has been of foremost importance as source of dispersal to the islands of the Western Indian Ocean. Following the colonization of Madagascar, rapid radiations appear to have taken place in some clades, and Madagascar has also been an important source area for subsequent dispersal to the Comoros, Mascarenes and Seychelles.
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| 9. |
- Karimu, Amin, 1978-, et al.
(författare)
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Who Adopts LPG as the Main Cooking Fuel and Why? : Empirical Evidence on Ghana Based on National Survey
- 2016
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Ingår i: World Development. - : Elsevier. - 0305-750X .- 1873-5991. ; 85, s. 43-57
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Tidskriftsartikel (refereegranskat)abstract
- The aim of this paper is to identify the factors that influence the probability of adopting LPG as the main cooking fuel in Ghana using household level data gleaned from last two nationwide household surveys (GLSS 5 & GLSS 6). Using a flexible semi parametric specification, the following were uncovered. First, we find socioeconomic and demographic factors such as income, education, access to urban infrastructure, and location of household, as key drivers of households' choice of LPG as main cooking energy source. Again the influences of these factors are stable across time, and with a strong price effect. The evidence shows that urban households with better socioeconomic and demographic factors are likely to adopt LPG as the main cooking fuel relative to households in rural areas and also urban households with poor socioeconomic and demographic factors. Finally, we observe that the imposition of fully parametric structure (functional form) prior to estimation on factors such as age of household head, income, and household size as done in the literature is inappropriate, at least in the case of Ghana and tend to bias the marginal effects. There is strong evidence of variations in the response rate of LPG adoption over the domains of income, household size, and the age of the household head. The results suggest a policy dichotomy between rural and urban dwellers for it to be effective.
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| 10. |
- Epstein, Seth, Researcher, 1978-
(författare)
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Flat Rat Taxicabs and the Production of Urban Space in Depression-Era Madison, Wisconsin
- 2021
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Ingår i: Journal of Historical Geography. - : Elsevier. - 0305-7488 .- 1095-8614. ; 71, s. 28-38
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Tidskriftsartikel (refereegranskat)abstract
- The Great Depression prompted a reconsideration of value in urban space. This occurred in the taxi industry when flat rates supplanted metered rates. The arrival of low fare flat rate taxis in Madison, Wisconsin in 1932 quickly led to a threefold increase in the number of cabs and the nearly complete cessation of cabs’ use of taximeters. Similar developments occurred elsewhere in U.S. cities during the 1930s. Earning the same fee for trips that varied in length and distance disrupted the homogeneity and abstraction of space and time which meters provided. The low fare flat rate system held out the promise of affordable transportation to passengers and economic self-sufficiency to drivers. However, despite its standardized rate, the space produced by participants in this system was characterized by unpredict- ability and uncertainty, as drivers sought to maximize their number of trips while minimizing the dis- tance and duration of each trip. The uncertainty generated by these efforts, the lower capital costs associated with the flat rate system, and a rise in customer demand led to a significant increase in taxicabs traveling city streets, which in turn made it more difficult for drivers to make a living. By examining the production of space engendered by the low fare flat rate system, this article demonstrates how the pressures of the Depression deepened the contradictions of capitalist political economy.
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