| 1. |
- Hillier, Ladeana W, et al.
(author)
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Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution
- 2004
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In: Nature. - 0028-0836 .- 1476-4687. ; 432:7018, s. 695-716
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Journal article (peer-reviewed)abstract
- We present here a draft genome sequence of the red jungle fowl, Gallus gallus. Because the chicken is a modern descendant of the dinosaurs and the first non-mammalian amniote to have its genome sequenced, the draft sequence of its genome--composed of approximately one billion base pairs of sequence and an estimated 20,000-23,000 genes--provides a new perspective on vertebrate genome evolution, while also improving the annotation of mammalian genomes. For example, the evolutionary distance between chicken and human provides high specificity in detecting functional elements, both non-coding and coding. Notably, many conserved non-coding sequences are far from genes and cannot be assigned to defined functional classes. In coding regions the evolutionary dynamics of protein domains and orthologous groups illustrate processes that distinguish the lineages leading to birds and mammals. The distinctive properties of avian microchromosomes, together with the inferred patterns of conserved synteny, provide additional insights into vertebrate chromosome architecture.
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| 2. |
- Schild, R., et al.
(author)
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Disparities in treatment and outcome of kidney replacement therapy in children with comorbidities: an ESPN/ERA Registry study
- 2023
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In: Clinical Kidney Journal. - : Oxford University Press (OUP). - 2048-8505 .- 2048-8513. ; 16:4, s. 745-755
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Journal article (peer-reviewed)abstract
- Background Data on comorbidities in children on kidney replacement therapy (KRT) are scarce. Considering their high relevance for prognosis and treatment, this study aims to analyse the prevalence and implications of comorbidities in European children on KRT. Methods We included data from patients <20 years of age when commencing KRT from 2007 to 2017 from 22 European countries within the European Society of Paediatric Nephrology/European Renal Association Registry. Differences between patients with and without comorbidities in access to kidney transplantation (KT) and patient and graft survival were estimated using Cox regression. Results Comorbidities were present in 33% of the 4127 children commencing KRT and the prevalence has steadily increased by 5% annually since 2007. Comorbidities were most frequent in high-income countries (43% versus 24% in low-income countries and 33% in middle-income countries). Patients with comorbidities had a lower access to transplantation {adjusted hazard ratio [aHR] 0.67 [95% confidence interval (CI) 0.61-0.74]} and a higher risk of death [aHR 1.79 (95% CI 1.38-2.32)]. The increased mortality was only seen in dialysis patients [aHR 1.60 (95% CI 1.21-2.13)], and not after KT. For both outcomes, the impact of comorbidities was stronger in low-income countries. Graft survival was not affected by the presence of comorbidities [aHR for 5-year graft failure 1.18 (95% CI 0.84-1.65)]. Conclusions Comorbidities have become more frequent in children on KRT and reduce their access to transplantation and survival, especially when remaining on dialysis. KT should be considered as an option in all paediatric KRT patients and efforts should be made to identify modifiable barriers to KT for children with comorbidities. Lay Summary Kidney transplantation (KT) is considered the optimal treatment for children who suffer from permanent kidney failure, because it leads to a lower mortality and higher quality of life compared with dialysis. Children on dialysis frequently suffer from diseases of other organs (comorbidities) that can directly lower their life expectancy and could potentially represent a barrier for transplantation, posing an additional disease burden for these children. In this study we looked at data from a large multinational registry for children with kidney failure who require kidney replacement. Using these data, we studied whether these children suffered from comorbidities and whether these impact their life expectancy or their access to KT. We found that more and more children with kidney failure suffer from comorbidities when starting kidney replacement therapy. We also found that these children have a lower access to KT and a higher mortality on dialysis compared with children without comorbidities, especially in low-income countries. After KT, children with comorbidities have a similar mortality and graft survival compared with children without comorbidities. We concluded that reduced access to a kidney transplant might represent a modifiable barrier to KT in children with comorbidities, especially in low-resource countries. We suggest that children with comorbidities in need for kidney replacement therapy should be rapidly evaluated for eligibility for KT.
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| 3. |
- Grankvist, Anna, et al.
(author)
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Multilocus sequence analysis of clinical "candidatus neoehrlichia mikurensis" strains from Europe
- 2015
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In: Journal of Clinical Microbiology. - 0095-1137 .- 1098-660X. ; 53:10, s. 3126-3132
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Journal article (peer-reviewed)abstract
- Copyright © 2015, American Society for Microbiology. All Rights Reserved. Candidatus Neoehrlichia mikurensis" is the tick-borne agent of neoehrlichiosis, an infectious disease that primarily affects immunocompromised patients. So far, the genetic variability of "Ca. Neoehrlichia" has been studied only by comparing 16S rRNA genes and groEL operon sequences. We describe the development and use of a multilocus sequence analysis (MLSA) protocol to characterize the genetic diversity of clinical "Ca. Neoehrlichia" strains in Europe and their relatedness to other species within the Anaplasmataceae family. Six genes were selected: ftsZ, clpB, gatB, lipA, groEL, and 16S rRNA. Each MLSA locus was amplified by real-time PCR, and the PCR products were sequenced. Phylogenetic trees of MLSA locus relatedness were constructed from aligned sequences. Blood samples from 12 patients with confirmed "Ca. Neoehrlichia" infection from Sweden (n9), the Czech Republic (n2), and Germany (n1) were analyzed with the MLSA protocol. Three of the Swedish strains exhibited identical lipA sequences, while the lipA sequences of the strains from the other nine patients were identical to each other. One of the Czech strains had one differing nucleotide in the clpB sequence from the sequences of the other 11 strains. All 12 strains had identical sequences for the genes 16S rRNA, ftsZ, gatB, and groEL. According to the MLSA, among the Anaplasmataceae, "Ca. Neoehrlichia" is most closely related to Ehrlichia ruminantium, less so to Anaplasma phagocytophilum, and least to Wolbachia endosymbionts. To conclude, three sequence types of infectious "Ca. Neoehrlichia" were identified: one in the west of Sweden, one in the Czech Republic, and one spread throughout Europe.
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| 4. |
- Dahlgren, Hanna, et al.
(author)
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Energy and flux variations across thin auroral arcs
- 2011
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In: Annales Geophysicae. - : Copernicus GmbH. - 0992-7689 .- 1432-0576. ; 29:10, s. 1699-1712
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Journal article (peer-reviewed)abstract
- Two discrete auroral arc filaments, with widths of less than 1 km, have been analysed using multi-station, multi-monochromatic optical observations from small and medium field-of-view imagers and the EISCAT radar. The energy and flux of the precipitating electrons, volume emission rates and local electric fields in the ionosphere have been determined at high temporal (up to 30 Hz) and spatial (down to tens of metres) resolution. A new time-dependent inversion model is used to derive energy spectra from EISCAT electron density profiles. The energy and flux are also derived independently from optical emissions combined with ion-chemistry modelling, and a good agreement is found. A robust method to obtain detailed 2-D maps of the average energy and number flux of small scale aurora is presented. The arcs are stretched in the north-south direction, and the lowest energies are found on the western, leading edges of the arcs. The large ionospheric electric fields (250 mV m(-1)) found from tristatic radar measurements are evidence of strong currents associated with the region close to the optical arcs. The different data sets indicate that the arcs appear on the boundaries between regions with different average energy of diffuse precipitation, caused by pitch-angle scattering. The two thin arcs on these boundaries are found to be related to an increase in number flux (and thus increased energy flux) without an increase in energy.
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| 5. |
- K. Franck, Anja, 1973, et al.
(author)
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I’ll tell you how it is: They treat us like slaves.” Non-citizenship, labor brokers and forced labor in Malaysia
- 2014
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In: 3rd Annual Southeast Asia Studies Symposium, 22-23 March 2014, Keble College, University of Oxford.
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Conference paper (other academic/artistic)abstract
- In Malaysia migration is highly politicized and securitized. Over the past few decades the large-scale in-migration of foreign workers has increasingly become constructed as a potential threat to national security – with policy emphasis being placed upon external and internal border control, and upon regulating and restricting the rights of non-citizens in the country. At the intersection of these politically motivated restrictions, the continued demand for foreign labour to fuel the country’s economy, and the continued need from people in (poorer) neighbouring countries to find employment abroad new actors emerge to facilitate both regular and irregular movement across the Malaysian border. Amongst the more important are labour outsourcing agencies (also known as labour brokers) which supply Malaysian employers with cheap foreign labour. Yet, despite their growing importance to the migration industry (in Malaysia and beyond) labour outsourcing agencies remain profoundly underresearched and few studies have examined the impact of their activities for the conditions of migrant workers in receiving countries. In this study emphasis is therefore placed upon migrant workers’ experiences of these agencies – in particular in relation to forced labour (understood as work performed under involuntary and coercive conditions). The study suggests that the outcome of the labour outsourcing system for forced labour needs to be understood in the context of the laws which regulate non-citizenship in Malaysia. It finds that the labour outsourcing system in combination with the weak (legal) bargaining position awarded to non-citizens in Malaysia (vis-à-vis employers, labour brokers and the state) produce not only vulnerability but also increase the risk of migrant workers ending up in forced labour.
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| 6. |
- K. Franck, Anja, 1973, et al.
(author)
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Navigating migrant trajectories through private actors: Burmese labour migration to Malaysia
- 2018
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In: European Journal of East Asian Studies. - : Brill. - 1568-0584 .- 1570-0615. ; 17:1, s. 55-82
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Journal article (peer-reviewed)abstract
- Recent research on the 'migration industry' has provided a means to interrogate how private actors come to be used as a means to facilitate, direct and control migration. Both through incorporating private actors into security functions and outsourcing certain functions to labour brokers, the use of migration industry actors is an important part of the ways in which the state works to maintain its sovereign control over territory and the ways people move across it. Yet this is not the only way in which migration industry actors are used. Instead, private actors also play a key role for migrants, although attention towards how migrants themselves perceive and use these actors during the migration process has received far less attention. Using timelines of migrant trajectories from Burma/Myanmar to Malaysia, the following study therefore sets out to map the private actors involved in the migrants' projects to travel to and stay in Malaysia - and to investigate how these actors are strategically used by migrants as a means to increase their room to manoeuvre during the migration process. In approaching this, the study combines literature on the privatisation and commercialisation of international migration with scholarship on migration trajectories and migrant agency. Empirically the study builds upon fieldwork conducted in the Burmese migrant community in the city of George Town in northern Malaysia.
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| 7. |
- Malmström, Helena, et al.
(author)
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Ancient DNA Reveals Lack of Continuitybetween Neolithic Hunter-Gatherersand Contemporary Scandinavians
- 2009
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In: Current Biology. - : Elsevier. - 0960-9822 .- 1879-0445. ; 19:20, s. 1758-1762
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Journal article (peer-reviewed)abstract
- The driving force behind the transition from a foraging to a farming lifestyle in prehistoric Europe (Neolithization) has been debated for more than a century [1–3]. Of particular interest is whether population replacement or cultural exchange was responsible [3–5]. Scandinavia holds a unique place in this debate, for it maintained one of the last major hunter-gatherer complexes in Neolithic Europe, the Pitted Ware culture [6]. Intriguingly, these late hunter-gatherers existed in parallel to early farmers for more than a millennium before they vanished some 4,000 years ago [7, 8]. The prolonged coexistence of the two cultures in Scandinavia has been cited as an argument against population replacement between the Mesolithic and the present [7, 8]. Through analysis of DNA extracted from ancient Scandinavian human remains, we show that people of the Pitted Ware culture were not the direct ancestors of modern Scandinavians (including the Saami people of northern Scandinavia) but are more closely related to contemporary populations of the eastern Baltic region. Our findings support hypotheses arising from archaeological analyses that propose a Neolithic or post-Neolithic population replacement in Scandinavia [7]. Furthermore, our data are consistent with the view that the eastern Baltic represents a genetic refugia for some of the European hunter-gatherer populations.
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| 8. |
- Parasyri, M., et al.
(author)
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Renal Phenotype in Mitochondrial Diseases: A Multicenter Study
- 2022
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In: Kidney Diseases. - : S. Karger AG. - 2296-9381 .- 2296-9357. ; 8:2
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Journal article (peer-reviewed)abstract
- Aims: This study aimed to investigate associations between renal and extrarenal manifestations of mitochondrial diseases and their natural history as well as predictors of renal disease severity and overall disease outcome. The secondary aim was to generate a protocol of presymptomatic assessment and monitoring of renal function in patients with a defined mitochondrial disease. Methods: A multicenter, retrospective cohort study was performed by the Mitochondrial Clinical and Research Network (MCRN). Patients of any age with renal manifestations associated with a genetically verified mitochondrial disease were included from 8 expert European centers specializing in mitochondrial diseases: Gothenburg, Oulu, Copenhagen, Bergen, Helsinki, Stockholm, Rotterdam, and Barcelona. Results: Of the 36 patients included, two-thirds had mitochondrial DNA-associated disease. Renal manifestations were the first sign of mitochondrial disease in 19%, and renal involvement was first identified by laboratory tests in 57% of patients. Acute kidney injury occurred in 19% of patients and was the first sign of renal disease in the majority of these. The most common renal manifestation was chronic kidney disease (75% with stage 2 or greater), followed by tubulopathy (44.4%), the latter seen mostly among patients with single large-scale mitochondrial DNA deletions. Acute kidney injury and tubulopathy correlated with worse survival outcome. The most common findings on renal imaging were increased echogenicity and renal dysplasia/hypoplasia. Renal histology revealed focal segmental glomerulosclerosis, nephrocalcinosis, and nephronophthisis. Conclusion: Acute kidney injury is a distinct renal phenotype in patients with mitochondrial disease. Our results highlight the importance to recognize renal disease as a sign of an underlying mitochondrial disease. Acute kidney injury and tubulopathy are 2 distinct indicators of poor survival in patients with mitochondrial diseases.
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| 9. |
- Westphal Ladfors, Susanne, et al.
(author)
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Long-lasting chronic high load carriage of Epstein-Barr virus is more common in young pediatric renal transplant recipients.
- 2020
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In: Pediatric nephrology. - : Springer Science and Business Media LLC. - 1432-198X .- 0931-041X. ; 35:3, s. 427-439
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Journal article (peer-reviewed)abstract
- Epstein-Barr virus (EBV) infections can induce post-transplant lymphoproliferative disorder (PTLD). A chronic high load (CHL), as indicated by long-term high EBV DNA levels after transplantation, has been associated with an enhanced risk of PTLD. We aimed to evaluate incidence, time of occurrence, risk factors, and outcome of EBV CHL carrier state after pediatric renal transplantation.A retrospective study of 58 children aged 1-17 years (median 10), who underwent renal transplantation between January 2004 and June 2017 at a single medical center. EBV IgG antibodies in serum were analyzed before and yearly after transplantation. EBV DNA in whole blood were analyzed weekly for the first 3 months post-transplant, monthly up to 1 year and then at least once yearly. CHL was defined as EBV DNA ≥ 4.2 log10 Geq/ml in > 50% of the samples during ≥ 6 months.At transplantation, 31 (53%) patients lacked EBV IgG and 25 (81%) of them developed primary EBV infection post-transplant. Of the 27 seropositive patients, 20 (74%) experienced reactivation of EBV. Altogether, 14 (24%) children developed CHL, starting at a median of 69 days post-transplant and lasting for a median time of 2.3 years (range 0.5-6.5), despite reduction of immunosuppression. Patients with CHL were younger and 11/14 were EBV seronegative at transplantation. No child developed PTLD during median clinical follow-up of 7.8 years (range 0.7-13).CHL was frequent, long lasting, and occurred mainly in young transplant recipients. The absence of PTLD suggests that monitoring of EBV DNA to guide immunosuppression was effective.
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| 10. |
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