| 1. |
- Bradnam, K. R., et al.
(författare)
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Assemblathon 2 : Evaluating de novo methods of genome assembly in three vertebrate species
- 2013
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Ingår i: GigaScience. - : BioMed Central (BMC). - 2047-217X. ; 2:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability, hardware requirements, acceptance of newer read technologies) and in their final output (composition of assembled sequence). More importantly, it remains largely unclear how to best assess the quality of assembled genome sequences. The Assemblathon competitions are intended to assess current state-of-the-art methods in genome assembly. Results: In Assemblathon 2, we provided a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and snake). This resulted in a total of 43 submitted assemblies from 21 participating teams. We evaluated these assemblies using a combination of optical map data, Fosmid sequences, and several statistical methods. From over 100 different metrics, we chose ten key measures by which to assess the overall quality of the assemblies. Conclusions: Many current genome assemblers produced useful assemblies, containing a significant representation of their genes and overall genome structure. However, the high degree of variability between the entries suggests that there is still much room for improvement in the field of genome assembly and that approaches which work well in assembling the genome of one species may not necessarily work well for another.
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| 2. |
- Ross, I L, et al.
(författare)
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Increased Cardiovascular Risk in South African Patients with Addison's Disease.
- 2013
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Ingår i: Hormone and metabolic research = Hormon- und Stoffwechselforschung = Hormones et métabolisme. - : Georg Thieme Verlag KG. - 1439-4286. ; 45:12, s. 905-10
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Tidskriftsartikel (refereegranskat)abstract
- Patients with Addison's disease (AD) are believed to be at risk for cardiovascular disease (CVD). South Africa, like the rest of the developing world is experiencing an increase in CVD and patients with AD may be at double the risk of their peers. We wished to explore AD patients' CVD risk factors. A cross-sectional nationwide study in South Africa of patients with AD was conducted. A cohort of 147 patients with AD and 147 healthy control subjects were matched by age, gender, ethnicity, and BMI as far as was possible. Lipoproteins and highly-sensitive C-reactive-protein (hs-CRP) were the main outcome measures. AD patients had significantly higher triglycerides; (p=0.001), lower HDLC (p<0.001), higher hs-CRP (p<0.001), and more small dense LDL; (p=0.002) than controls. Nonesterified fatty acids were lower in patients (p<0.001). Approximately 65% [95% confidence interval (CI 55.6-72.4%)] had hypercholesterolaemia, 75% (CI 64.8-81.2%) had low HDLC, and 75% (CI 68.0-84.1%) had a higher LDLC. Thirteen percent of AD patients had diabetes mellitus, but none of the risk factors differed from the nondiabetics. Only HDLC correlated positively with daily hydrocortisone dose (r=0.32; p=0.005). In conclusion dyslipidaemia is common in South African AD patients; CVD risk assessment and intervention are probably warranted in the management of these patients.
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| 3. |
- Ross, I. L., et al.
(författare)
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Investigation of glucocorticoid receptor polymorphisms in relation to metabolic parameters in Addison's disease
- 2013
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Ingår i: European Journal of Endocrinology. - 0804-4643 .- 1479-683X. ; 168, s. 403-412
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Tidskriftsartikel (refereegranskat)abstract
- Background Uncertainty exists whether glucocorticoid receptor (GCR) polymorphisms play a role in steroid-related side effects in Addison's disease (AD) patients on hydrocortisone. The polymorphisms Bcll and N363S appear to increase sensitivity to cortisol, while the ER22/23EK polymorphism has been associated with resistance to cortisol. Method One hundred and forty seven AD patients, and gender, and ethnicity-matched controls were recruited in South Africa. Three polymorphisms in the GCR were studied, using PCR followed by restriction fragment length analysis. Associations with BMI, lipids, glucose and inflammatory markers were investigated. Results In both patients and controls, the Bcll polymorphism occurred more frequently in whites than in other ethnic groups studied but was not associated with any of the metabolic parameters tested. The ER22/23EK polymorphism was associated with an increased BMI in both patients (29.4 vs 24.7kg/m2) and control subjects (26.3 vs 24.2kg/m2). The ER22/23EK polymorphism was also associated with lower LDL cholesterol in control subjects (3.46 vs 3.93mmol/l) and in patients (3.52 vs 4.10mmol/l). N363S was associated with increased BMI in controls 29.9kg/m2 vs wild type 24.8kg/m2. Median hydrocortisone doses were greater in patients heterozygous for either ER22/23EK 30.0mg or N363S 25.0mg polymorphisms than in wild type patients 20.0mg (both comparisons). Conclusion Alterations in lipids, BMI and hydrocortisone dose were associated with two polymorphisms. Further larger studies are warranted to corroborate these findings.
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| 4. |
- Ross, I. L., et al.
(författare)
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Salivary Cortisol Day Curves in Addison's Disease in Patients on Hydrocortisone Replacement
- 2013
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Ingår i: Hormone and Metabolic Research. - : Georg Thieme Verlag KG. - 0018-5043 .- 1439-4286. ; 45:1, s. 62-68
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Tidskriftsartikel (refereegranskat)abstract
- Using salivary cortisol (SC) measurements, cortisol exposure in Addison's disease patients on hydrocortisone replacement was determined and compared with healthy controls. Cortisol pharmacokinetics was assessed in 31 patients with Addison's disease on replacement hydrocortisone doses ( median daily dose 20mg; range 5-50mg) and 30 healthy control subjects. Saliva samples (n=16) were collected between 08:00 and 00:00h in 1 day, using a passive drool technique. Cortisol exposure was evaluated by noncompartmental approach. In the patients, cortisol exposure was significantly higher than in controls: median inter-quartile range (IQR) peak cortisol (C-max ) 174.5 (59.3-837.0) vs. 6.50 (4.7-19.3) nmol/l, p=0.0001; area under the curve (AUC) 390.1 (177.1-928.9) vs. 21.4 (14.6-28.4) minutes*nmol/l, p=0.0001, trough cortisol level (C-min) 0.49 (0.49-0.96) vs. 0.49 (0.49-0.49) nmol/l, p=0.02, occurring at 480.0 (0.1- 660.0) vs. 405.0 (180.0-570.0) min, p=0.56. First peak cortisol was 174.5 (53.0-754.7) vs. 6.27 (3.90-8.47 ) nmol/l, p=0.0001 and second peak cortisol 18.90 (5.22-76.9) vs. 3.12 (1.76-4.79) nmol/l, p=0.0001. The time to first peak cortisol differed between the 2 groups, 30 (30-75) vs. 0.1 (0.1-30) minutes; p=0.0001. At doses studied, hydrocortisone replacement therapy results in cortisol pharmacokinetics being markedly different from endogenous cortisol profiles in healthy control subjects. Addison's disease patients had significantly higher SC levels compared to healthy control subjects.
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| 5. |
- Coulson, S. J., et al.
(författare)
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Introduction of invertebrates into the High Arctic via imported soils: the case of Barentsburg in the Svalbard
- 2013
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Ingår i: Biological Invasions. - : Springer Science and Business Media LLC. - 1387-3547 .- 1573-1464. ; 15:1, s. 1-5
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Tidskriftsartikel (refereegranskat)abstract
- Forty six species of invertebrate were collected from the manure enriched imported soils below the abandoned cow sheds in the Russian mining town of Barentsburg, Svalbard. Of these, 11 (24 %) were new records for Svalbard, including Collembola, gamasid mites, Enchytraeidae and the first identified Lumbricidae. Many of the new records are species not frequently observed in the Arctic. It is hypothesized that these species arrived with the chernozem soils imported to Barentsburg for the greenhouses from central or southern European Russia, or with livestock. The observations presented here are the first records of human invertebrate introductions establishing in Svalbard outside of dwellings. It is not believed that the majority of new species records described present an immediate threat to the ecology of Svalbard but they may, especially Deuteraphorura variabilis, establish in the nutrient enriched floral communities beneath bird cliffs characteristic of Svalbard.
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| 6. |
- Coulson, S. J., et al.
(författare)
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The invertebrate fauna of anthropogenic soils in the High-Arctic settlement of Barentsburg, Svalbard
- 2013
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Ingår i: Polar Research. - : Norwegian Polar Institute. - 0800-0395 .- 1751-8369. ; 32
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Tidskriftsartikel (refereegranskat)abstract
- The terrestrial environment of the High Arctic consists of a mosaic of habitat types. In addition to the natural habitat diversity, various human-influenced types may occur. For the resident invertebrate fauna, these anthropogenic habitats may be either unusually favourable or detrimental. In the town of Barentsburg, Svalbard, soils were imported for the greenhouses from southern Russia. These soils were subsequently discarded outside the greenhouses and have become augmented with manure from the cowsheds. Both the greenhouse and the cowsheds are now derelict. This site represents an unusually nutrient-rich location with considerable development of organic soils, in stark contrast to the naturally forming organic soils in Svalbard, which are typically thin and nutrient poor. Few previous studies have examined the soil invertebrate communities of human-disturbed or -created habitats in the Arctic. In an often nutrient-poor terrestrial environment, it is unclear how the invertebrate fauna will react to such nutrient enhancement. In these soils, 46 species of invertebrates were determined. Eleven species have not been recorded from other habitats in Svalbard and are hence likely to have been introduced. The native species assemblage in the anthropogenic soils was not atypical for many natural sites in Svalbard. Despite the enriched organic soils and highly ameliorated winter temperature conditions, the soil invertebrate fauna biodiversity does not appear to be enhanced beyond the presence of certain probably introduced species.
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| 7. |
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| 8. |
- Sterner, Y, et al.
(författare)
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Country-specific birth weight and length in type 1 diabetes high-risk HLA genotypes in combination with prenatal characteristics.
- 2011
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Ingår i: Journal of Perinatology. - : Springer Science and Business Media LLC. - 0743-8346 .- 1476-5543. ; 31, s. 764-769
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Tidskriftsartikel (refereegranskat)abstract
- Objective:To examine the relationship between high-risk human leukocyte antigen (HLA) genotypes for type 1 diabetes and birth size in combination with prenatal characteristics in different countries.Study Design:Four high-risk HLA genotypes were enrolled in the Environmental determinants of Diabetes in the Young study newborn babies from the general population in Finland, Germany, Sweden and the United States. Stepwise regression analyses were used to adjust for country, parental physical characteristics and environmental factors during pregnancy.Result:Regression analyses did not reveal differences in birth size between the four type 1 diabetes high-risk HLA genotypes. Compared with DQ 4/8 in each country, (1) DQ 2/2 children were heavier in the United States (P=0.028) mostly explained however, by parental weight; (2) DQ 2/8 (P=0.023) and DQ 8/8 (P=0.046) children were longer in Sweden independent of parents height and as well as (3) in the United States for DQ 2/8 (P=0.023), but again dependent on parental height.Conclusion:Children born with type 1 diabetes high-risk HLA genotypes have comparable birth size. Longitudinal follow-up of these children should reveal whether birth size differences between countries contribute to the risk for islet autoimmunity and type 1 diabetes.Journal of Perinatology advance online publication, 28 April 2011; doi:10.1038/jp.2011.26.
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