| 1. |
- Zamani, Neda, et al.
(författare)
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Unsupervised genome-wide recognition of local relationship patterns
- 2013
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Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 14, s. 347-
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUNDPhenomena such as incomplete lineage sorting, horizontal gene transfer, gene duplication and subsequent sub- and neo-functionalisation can result in distinct local phylogenetic relationships that are discordant with species phylogeny. In order to assess the possible biological roles for these subdivisions, they must first be identified and characterised, preferably on a large scale and in an automated fashion.RESULTSWe developed Saguaro, a combination of a Hidden Markov Model (HMM) and a Self Organising Map (SOM), to characterise local phylogenetic relationships among aligned sequences using cacti, matrices of pair-wise distance measures. While the HMM determines the genomic boundaries from aligned sequences, the SOM hypothesises new cacti in an unsupervised and iterative fashion based on the regions that were modelled least well by existing cacti. After testing the software on simulated data, we demonstrate the utility of Saguaro by testing two different data sets: (i) 181 Dengue virus strains, and (ii) 5 primate genomes. Saguaro identifies regions under lineage-specific constraint for the first set, and genomic segments that we attribute to incomplete lineage sorting in the second dataset. Intriguingly for the primate data, Saguaro also classified an additional ~3% of the genome as most incompatible with the expected species phylogeny. A substantial fraction of these regions was found to overlap genes associated with both the innate and adaptive immune systems.CONCLUSIONSSaguaro detects distinct cacti describing local phylogenetic relationships without requiring any a priori hypotheses. We have successfully demonstrated Saguaro's utility with two contrasting data sets, one containing many members with short sequences (Dengue viral strains: n = 181, genome size = 10,700 nt), and the other with few members but complex genomes (related primate species: n = 5, genome size = 3 Gb), suggesting that the software is applicable to a wide variety of experimental populations. Saguaro is written in C++, runs on the Linux operating system, and can be downloaded from http://saguarogw.sourceforge.net/.
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| 2. |
- Fernström, Lise-Lotte, et al.
(författare)
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Presence of pathogenic bacteria in faeces from dogs fed raw meat-based diets or dry kibble
- 2020
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Ingår i: Veterinary Record. - : Wiley. - 0042-4900 .- 2042-7670. ; 187
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Tidskriftsartikel (refereegranskat)abstract
- Background Feeding dogs with raw meat-based diets (RMBD) has increased in popularity in recent years. Proponents claim that RMBD is more natural for dogs, because it is what their ancestors (wolves) eat. Opponents claim that RMBD is a health hazard to both humans and animals, with a risk of spreading zoonotic bacteria and resistant bacterial strains.Methods This cross-sectional study investigated differences in bacteria shedding in faeces between dogs fed RMBD and dogs fed dry kibble. Faeces samples from 50 dogs from the same municipality were analysed for the presence of extended-spectrum beta-lactamases (ESBL)-producing Escherichia coli, Campylobacter and Salmonella.Results For the 25 dogs fed RMBD, ESBL E coli was isolated from 13 faeces samples, Campylobacter from 12 and Salmonella from 1. For the 25 dogs fed dry kibble, ESBL-producing E coli was isolated from one faeces sample and Campylobacter from four, while Salmonella was not detected.Conclusion There was thus a significant difference in excretion of zoonotic and resistant bacteria in faeces between dogs fed RMBD and dogs fed dry kibble. These results confirm that RMBD can pose a microbiological risk not only for dogs, but also for people handling RMBD and faeces from dogs.
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| 3. |
- Klinthäll, Martin, 1967-
(författare)
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Etnisk bakgrund, integration och sjuklighet : Slutenvård bland invandrare i Sverige 1990–2001
- 2007
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Ingår i: Working Papers in Social Insurance. - Stockholm : Försäkringskassan. - 1653-1353. ; :1, s. 1-28
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Objectives: The purpose of this study is to analyze to what extent differences in health between groups of different origin remain after considering differences in education, income and labor market status, and whether there exists any patterns according to the socioeconomic character of the country of origin. Design: The study is based on two data sources; Longitudinal Database for Education, Income and Employment, (LOUISE) and the Hospital Discharge Register (HDR). The data set consists of all Swedish and foreign born individuals born in 1945, 1955 and 1965, who were Swedish residents in 1990. The risk of hospitalization is analyzed for the period 1990–2001 using binomial logit regression. Results: When only demographic characteristics are controlled for, most immigrant groups display higher rates of hospital discharge records than native Swedes, but when education, income and labor market status is introduced into the model, only Nordic immigrants display levels of severe morbidity that are significantly higher than the levels for Swedish born. Among welfare recipients, only immigrants from Finland display higher levels of severe morbidity than native Swedes; most immigrant groups display significantly lower levels of severe morbidity than native Swedes. The analysis shows no evidence of a systematic relationship between health status and the socioeconomic character of the country of origin. Conclusion: Higher levels of severe morbidity among immigrants compared to Swedes seem to be explained by the socioeconomic situation in Sweden, rather than health conditions and socioeconomic circumstances before immigration. There is a strong correlation between a weak labor market integration and high levels of severe morbidity in non-Nordic immigrant groups.
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| 4. |
- Mantalos, Panagiotis, et al.
(författare)
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Size and Power of the Error Correction Model (ECM) of Cointegration Tests. A Bootstrap Approach
- 1998
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Ingår i: Oxford Bulletin of Economics and Statistics. - : John Wiley & Sons. - 0305-9049 .- 1468-0084. ; 60:2, s. 249-255
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Tidskriftsartikel (refereegranskat)abstract
- The size and power of the ECM cointegration test are investigated by using the ‘bootstrap critical values’. The purpose of this paper is to show the ability of the bootstrap technique to produce critical values which are much more accurate than the asymptotic ones. The properties of the test have been studied, using Monte Carlo methods, for three different data generating processes. As regards the size of the test, we find that the ECM cointegration test together with the bootstrap critical values perform better than the ECM cointegration test based on the asymptotic critical values. While as regards the power of the tests, the results prove to be similar for the different versions.
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| 5. |
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| 6. |
- Dong, Yan, et al.
(författare)
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Probing Exocytosis at Single Cells using Electrochemistry
- 2010
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Ingår i: Chemical Cytometry: Ultrasensive Analysis of Single Cells (ed C. Lu). - Weinheim : Wiley-VCH Verlag GmbH & Co.. - 9783527324958 ; , s. 159-174
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Bokkapitel (övrigt vetenskapligt/konstnärligt)
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| 7. |
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| 10. |
- Beach, Hugh
(författare)
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Samerna får eget parlament
- 1994
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Ingår i: Året i Focus 1993. - : Norstedts Förlag, Stockholm, och Bra Böcker AB, Höganäs.
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Bokkapitel (populärvet., debatt m.m.)
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| 11. |
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| 14. |
- Garcia, Angel, 1984, et al.
(författare)
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A Metric on the Space of Finite Sets of Trajectories for Evaluation of Multi-Target Tracking Algorithms
- 2020
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Ingår i: IEEE Transactions on Signal Processing. - 1941-0476 .- 1053-587X. ; 68, s. 3917-3928
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Tidskriftsartikel (refereegranskat)abstract
- In this article, we propose a metric on the space of finite sets of trajectories for assessing multi-target tracking algorithms in a mathematically sound way. The main use of the metric is to compare estimates of trajectories from different algorithms with the ground truth of trajectories. The proposed metric includes intuitive costs associated to localization error for properly detected targets, missed and false targets and track switches at each time step. The metric computation is based on solving a multi-dimensional assignment problem. We also propose a lower bound for the metric, which is also a metric for sets of trajectories and is computable in polynomial time using linear programming. We also extend the proposed metrics on sets of trajectories to random finite sets of trajectories.
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| 15. |
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| 17. |
- Phaijit, Ornnalin, et al.
(författare)
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A Demonstration of the Taxonomy of Functional Augmented Reality for Human-Robot Interaction
- 2022
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Ingår i: ACM/IEEE International Conference on Human-Robot Interaction. - 2167-2148. ; 2022-March, s. 981-985
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Konferensbidrag (refereegranskat)abstract
- With the rising use of Augmented Reality (AR) technologies in Human-Robot Interaction (HRI), it is crucial that HRI research examines the role of AR in HRI to better define AR-HRI systems and identify potential areas for future research. A taxonomy for AR in HRI has recently been proposed for the field. However, it was limited to the definition of the framework, and exemplifying its use was missing. In this paper, we perform a demonstration of how the aforementioned taxonomy of AR in HRI can be used to analyse an existing AR-HRI system and come up with questions for alternative ways AR-HRI could be designed and further extended.
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| 18. |
- Vorburger, Audrey, et al.
(författare)
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Three‐Dimensional Modeling of Callisto's Surface Sputtered Exosphere Environment
- 2019
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Ingår i: Journal of Geophysical Research - Space Physics. - 2169-9380 .- 2169-9402. ; 124:8, s. 7157-7169
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Tidskriftsartikel (refereegranskat)abstract
- We study the release of various elements from Callisto's surface into its exosphere by plasma sputtering. The cold Jovian plasma is simulated with a 3‐D plasma‐planetary interaction hybrid model, which produces 2‐D surface precipitation maps for magnetospheric H+, O+, O++, and S++. For the hot Jovian plasma, we assume isotropic precipitation onto the complete spherical surface. Two scenarios are investigated: one where no ionospheric shielding takes place and accordingly full plasma penetration is implemented (no‐ionosphere scenario) and one where an ionosphere lets virtually none of the cold plasma but all of the hot plasma reach Callisto's surface (ionosphere scenario). In the 3‐D exosphere model, neutral particles are sputtered from the surface and followed on their individual trajectories. The 3‐D density profiles show that whereas in the no‐ionosphere scenario the ram direction is favored, the ionosphere scenario produces almost uniform density profiles. In addition, the density profiles in the ionosphere scenario are reduced by a factor of ∼2.5 with respect to the no‐ionosphere scenario. We find that the Neutral Gas and Ion Mass Spectrometer, which is part of the Particle Environment Package on board the JUpiter ICy moons Explorer mission, will be able to detect the different sputter populations from Callisto's icy surface and the major sputter populations from Callisto's nonicy surface. The chemical composition of Callisto's exosphere can be directly linked to the chemical composition of its surface and will offer us information not only on Callisto's formation scenario but also on the building blocks of the Jupiter system.
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| 19. |
- Ademark, Pia, et al.
(författare)
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Multiple alpha-galactosidases from Aspergillus niger: purification, characterization, and substrate specificities
- 2001
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Ingår i: Enzyme and Microbial Technology. - 0141-0229. ; 29:6-7, s. 441-448
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Tidskriftsartikel (refereegranskat)abstract
- Enzymes with α-galactosidase activity are produced by many organisms, often in multiple forms. Here we compare the biochemical and hydrolytic properties of four major α-galactosidase forms (α-gal I-IV) that were purified from the culture filtrate of Aspergillus niger. α-Gal II, III and IV appear to be isoforms of the same enzyme, and N-terminal amino acid sequence data suggest that they are closely related or identical to A. niger AglB in family 27 of the glycosyl hydrolases. α-Gal I is a completely different enzyme that belongs to family 36. α-Gal I had an isoelectric point of 4.15 and appears to be a tetramer composed of four 94-kDa subunits. α-Gal II, III and IV were dimers with monomeric molecular masses of 64 kDa and isoelectric points of 4.5, 4.7 and 4.8, respectively. α-Gal II-IV were stable when incubated for 17 h at 50°C and pH 2–5, whereas α-gal I was most stable at pH 5–6. All enzymes had maximal catalytic activity at pH 4.5 and 60°C, and hydrolyzed melibiose, raffinose and stachyose. α-Gal II-IV also degraded galactomanno-oligosaccharides and released 66% of the galactose side groups from polymeric locust bean gum galactomannan. α-Gal I released galactose from locust bean gum only in combination with A. niger β-mannosidase. Kinetic experiments showed that α-gal I hydrolyzed p-nitrophenyl-α-Image-galactopyranoside and melibiose more efficiently than α-gal II-IV. The distinct hydrolytic and biochemical properties of α-gal I and α-gal II-IV further signifies the difference between α-galactosidases of family 27 and 36.
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| 20. |
- Agthe, Michael, et al.
(författare)
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Following the Assembly of Iron Oxide Nanocubes by Video Microscopy and Quartz Crystal Microbalance with Dissipation Monitoring
- 2017
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Ingår i: Langmuir. - : American Chemical Society (ACS). - 0743-7463 .- 1520-5827. ; 33:1, s. 303-310
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Tidskriftsartikel (refereegranskat)abstract
- We have studied the growth of ordered arrays by evaporation-induced self-assembly of iron oxide nanocubes with edge lengths of 6.8 and 10.1 nm using video microscopy (VM) and quartz crystal microbalance with dissipation monitoring (QCM-D). Ex situ electron diffraction of the ordered arrays demonstrates that the crystal axes of the nanocubes are coaligned and confirms that the ordered arrays are mesocrystals. Time-resolved video microscopy shows that growth of the highly ordered arrays at slow solvent evaporation is controlled by particle diffusion and can be described by a simple growth model. The growth of each mesocrystal depends only on the number of nanoparticles within the accessible region irrespective of the relative time of formation. The mass of the dried mesocrystals estimated from the analysis of the bandwidth-shift-to-frequency-shift ratio correlates well with the total mass of the oleate-coated nanoparticles in the deposited dispersion drop.
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| 23. |
- Alvarez, Pilar
(författare)
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De sobremesa 1887-1896 : José Asunción Silva:El poeta novelista
- 2004
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- José Asunción Silva is a Colombian poet most known for having renewed the metrics in Spanish poetry during the 19th century. José Asunción Silva's only novel, De sobremesa 1887-1896 [After dinner, 1887-1896] written in 1896 is a significant and representative modernist novel in the tradition of Latin-American modernismo.Silvas novel has been considered as a structureless, narratively disordered and chaotic text by many literary critics since its first publication in 1925. The text presents a great deal of fragmentation on the surface level: the story is presented by means of temporal discontinuity and multiple narrative voices and its thematic richness seems to be endless. The characters reveal multiple perspectives and a plurality of discourses.This dissertation determines and analyzes the formal and thematic aspects of the text that underlie its apparently disordered structure. The analysis focuses on the study of the referentiality of the text and some of its narrative components. It examines how the different fragments of the story, which are apparently neither logically nor thematically ordered on the surface level, are associated and integrated in the novel as a whole.Silva as a novelist makes use of some of the conventions of poetry and the techniques he applied to his poems. Contrast, association, assimilation and parallelisms are ways of creating new organizational forms of expressions in his prose work. The protagonist of De sobremesa, himself a poet, also plays the role of author, narrator, narratee and reader of his own prose work, his personal diary. This is a very particular feature in the context of Latin-American modernist novels written between 1882- 1902. The study analyzes the different roles of the character in the story to prove that the sense of unity is built by centring the text technically and thematically on the protagonist in its different roles. Silva makes the protagonist the point of convergence of the whole text.This dissertation suggests that there is an organized structure underlying the apparent disorder and incoherence of the text. The basis for Silvas text is diversity and the different where even the smallest parts prove to correspond with a bigger one. For a text of the 19th century, this is an innovative and experimental way of writing that seeks to create unity out of disorder and fragmentation.
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| 24. |
- Antonijevic, Sasa, et al.
(författare)
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Study of water dynamics and distances in paramagnetic solids by variable-temperature two-dimensional H-2 NMR spectroscopy
- 2007
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 126:1
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Tidskriftsartikel (refereegranskat)abstract
- A recently proposed two-dimensional H-2 NMR experiment is used to measure the H-2 (spin I=1) quadrupolar and paramagnetic shift anisotropy interactions in powdered CuCl2 center dot 2D(2)O as a function of temperature. The principal components of the quadrupolar and paramagnetic shift anisotropy tensors and the Euler angles describing the orientations of the tensors in the molecular frame are determined at each temperature. For this purpose an analytical approach is introduced to extract desired parameters from motionally averaged two-dimensional line shapes where the averaging is introduced by rapid 180 degrees flips around C-2 axes of D2O molecules. This approach can be readily applied to study various materials containing water of crystallization. It is also clearly shown that the rapid continuous rotation of D2O molecules around their C-2 axes is not taking place in the studied solid in the range of temperatures between 209 and 344 K. Once the paramagnetic shift anisotropy of a deuterium atom is measured accurately it is used to estimate the distance between deuterium and the nearest copper atom bearing an unpaired electron. Excellent agreement is found between structural parameters obtained in this study and those provided by neutron and x-ray diffraction, showing that the paramagnetic shift anisotropy is a sensitive probe of distances in paramagnetic solids. (c) 2007 American Institute of Physics.
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