| 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. |
- Erenpreiss, Juris, et al.
(författare)
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The impact of androgen receptor polymorphism and parental ethnicity on semen quality in young men from Latvia
- 2008
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Ingår i: International Journal of Andrology. - : Wiley. - 0105-6263 .- 1365-2605. ; 31:5, s. 477-482
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Tidskriftsartikel (refereegranskat)abstract
- Recent studies on young men from the general population have demonstrated geographic and ethnic differences in semen quality. The aim of this study was to investigate whether reported ethnic differences in semen quality might be associated with the maternally derived CAG and GGN polymorphisms in the androgen receptor gene or paternal ethnicity. In total 114 military conscripts from Latvia were included in the study. Information on maternal and parental ethnicity was collected by questionnaires. CAG and GGN repeats were analysed by direct sequencing of leukocyte DNA. Men with Latvian mothers (n = 83) had marginally shorter CAG repeat length (21.6 +/- 2.9) as compared with those with non-Latvian mothers (22.9 +/- 3.2, n = 31), not reaching statistical significance (p = 0.053). Sperm concentration did not differ significantly between these two groups (76 +/- 59 and 70 +/- 52, p = 0.9 respectively). In contrast, significantly higher sperm concentration and total sperm count were found in men with Latvian fathers (n = 77) as compared with men with non-Latvian fathers (n = 37) (80 +/- 61 vs. 62 +/- 48, p = 0.035, for sperm concentration and 225.7 +/- 209 vs. 158.4 +/- 134.4, p = 0.002, for total sperm count respectively). CAG repeat length did not correlate with any semen parameters in the whole population. However, GGN repeat length correlated with semen volume: men with GGN > 23 presented with higher semen volume (3.2 +/- 2.1) as compared with men with GGN = 23 (2.6 +/- 1.3, p = 0.04) or GGN < 23 (2.0 +/- 1.2, p = 0.006). We conclude that GGN repeat length has an impact on semen volume, whereas differences in sperm numbers are associated with the paternal ethnicity.
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| 3. |
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| 4. |
- Tsarev, I., et al.
(författare)
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Evaluation of male fertility potential by Toluidine Blue test for sperm chromatin structure assessment
- 2009
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Ingår i: Human Reproduction. - : Oxford University Press (OUP). - 0268-1161 .- 1460-2350. ; 24:7, s. 1569-1574
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Tidskriftsartikel (refereegranskat)abstract
- We have previously suggested that the Toluidine Blue (TB) test can be used for sperm chromatin structure assessment. In this study, we wished to evaluate the clinical applicability of the TB test in assessing male fertility potential using well-defined groups of fertile and infertile men. Sixty-three fertile and 79 infertile men were tested. Infertility thresholds for the proportion of sperm with abnormal [TB dark cells (TBDCs)] and normal [TB light cells (TBLCs)] chromatin structure were set by the ROC curve analysis. Thresholds of 45% TBDC and 20% TBLC were highly predictive for infertility (specificity of the test: 92 and 90%, respectively), but they were poor predictors of the fertility (sensitivity of the test: 42 and 32%, respectively). Odds ratio for infertility was 7.5 [95% confidence interval (CI): 2.7-20.8] when the 45% TBDC threshold was used and 4.4 (95% CI: 1.7-11.6) when the 20% TBLC threshold was used. The TB test can be suggested for clinical use as a complementary test for standard semen analysis to diagnose male infertility.
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| 5. |
- Tsarev, I, et al.
(författare)
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Sperm concentration in Latvian military conscripts as compared with other countries in the Nordic-Baltic area
- 2005
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Ingår i: International Journal of Andrology. - : Wiley. - 0105-6263 .- 1365-2605. ; 28:4, s. 208-214
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Tidskriftsartikel (refereegranskat)abstract
- Recent studies of semen quality in men from the general population gave rise to the hypothesis of an East-West gradient in semen quality in the Nordic-Baltic area, with the highest sperm counts in Estonia, Lithuania and Finland, and the lowest in Denmark (30% difference in mean concentration). Genetic, lifestyle-related and environmental factors - alone or in combination - were suggested to be responsible for these differences. The aim of this study was to assess sperm concentration in men from the general population in Latvia and to investigate the impact of ethnic and lifestyle-related factors on this marker of male reproductive health. A total of 133 military conscripts from Latvia were investigated. We found that sperm counts among Latvian adolescents were at the same level (mean 74, median 63 x 10(6)/mL) as those previously reported from Estonia, Lithuania and Finland. Sperm concentration was somewhat higher than in Sweden without reaching the level of statistical significance (mean difference 3 x 10(6)/mL; 95% CI: -10, 16 x 10(6)/mL), and statistically significantly higher that in Denmark (mean difference: 17 x 10(6)/mL; 95% CI: 5, 2 x 10(6)/mL). The study also revealed an impact of ethnic factors on sperm numbers. Sperm concentration was significantly higher in men with both parents born in Latvia (77 +/- 60 x 10(6)/mL), compared with men with both parents born outside Latvia (55 +/- 45 x 10(6)/mL, p = 0.03).
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